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AtTOME: Gene Expression Atlas Data Sources ( Aug. 2, 2016 ) |
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1: GSE8365 record: Identification of circadian-regulated genes of Arabidopsis thaliana. [Arabidopsis thaliana]
Summary: Most higher organisms, including plants and animals, have developed a time-keeping mechanism that allows them to anticipate daily fluctuations of environmental parameters such as light and temperature. This circadian clock efficiently coordinates plant growth and metabolism with respect to time-of-day by producing self-sustained rhythms of gene expression with an approximately 24-hour period. The importance of these rhythms has in fact been demonstrated in both phytoplankton and higher plants: organisms that have an internal clock period matched to the external environment possess a competitive advantage over those that do not. We used microarrays to identify circadian-regulated genes of Arabidopsis thaliana to elucidate how the clock provides an adaptive advantage by understanding how . Samples: 12 GSM207286: Seedling_ConstantWhiteLight_24hr GSM207287: Seedling_ConstantWhiteLight_28hr GSM207288: Seedling_ConstantWhiteLight_32hr GSM207289: Seedling_ConstantWhiteLight_36hr GSM207290: Seedling_ConstantWhiteLight_40hr GSM207291: Seedling_ConstantWhiteLight_44hr GSM207292: Seedling_ConstantWhiteLight_48hr GSM207293: Seedling_ConstantWhiteLight_52hr GSM207294: Seedling_ConstantWhiteLight_56hr GSM207295: Seedling_ConstantWhiteLight_60hr GSM207296: Seedling_ConstantWhiteLight_64hr GSM207297: Seedling_ConstantWhiteLight_68hr 2: GSE7432 record: Ethylene and auxin interactions in the roots of Arabidopsis seedlings [Arabidopsis thaliana] Summary: Understanding how developmental and environmental signals are integrated to produce specific responses is one of the main challenges of modern biology. Hormones and, most importantly, interactions between different hormones serve as crucial regulators of plant growth and development, playing central roles in the coordination of internal developmental processes with the environment. Herein, a combination of physiological, genetic, cellular, and whole-genome expression profiling approaches has been employed to investigate the mechanisms of interaction between two key plant hormones, ethylene and auxin. Quantification of the morphological effects of ethylene and auxin in a variety of mutant backgrounds indicates that auxin biosynthesis, transport, signaling and response are required for the ethylene-induced growth inhibition in roots but not in hypocotyls. Samples: 16 GSM179958: Arabidopsis roots, air treatment, replica 1 GSM179959: Arabidopsis roots, air treatment, replica 2 GSM179960: Arabidopsis roots, ethylene treatment, replica 1 GSM179961: Arabidopsis roots, ethylene treatment, replica 2 GSM179963: Arabidopsis aux1 mutant roots, air treatment, replica 1 GSM179967: Arabidopsis aux1 mutant roots, air treatment, replica 2 GSM179969: Arabidopsis aux1 mutant roots, ethylene treatment, replica 1 GSM179970: Arabidopsis aux1 mutant roots, ethylene treatment, replica 2 GSM179971: Arabidopsis roots, mock treatment, replica 1 GSM179972: Arabidopsis roots, mock treatment, replica 2 GSM179973: Arabidopsis roots, IAA treatment, replica 1 GSM179974: Arabidopsis roots, IAA treatment, replica 2 GSM179975: Arabidopsis ein2 mutant roots, mock treatment, replica 1 GSM179976: Arabidopsis ein2 mutant roots, mock treatment, replica 2 GSM179977: Arabidopsis ein2 mutant roots, IAA treatment, replica 1 GSM179978: Arabidopsis ein2 mutant roots, IAA treatment, replica 2 3: GSE8279 record: CG Methylation Stabilizes Epigenetic Inheritance by Preventing Aberrant DNA and Histone Methylation [Arabidopsis thaliana] Summary: Maintenance of CG methylation (mCG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining mCG, we found that mCG loss triggered genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms involving RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation act in a stochastic and uncoordinated fashion. As a result, new and aberrant epigenetic patterns were progressively formed over several plant generations in the absence of mCG. Interestingly, the unconventional redistribution of epigenetic marks was necessary to ?rescue? the loss of mCG, since mutant plants impaired in rescue activities were severely dwarfed and sterile. Samples: 6 GSM205364: met1-3_leaf_second-selfed generation_rep01 GSM205426: met1-3_leaf_second-selfed generation_rep02 GSM205428: met1-3_leaf_fourth-selfed generation_rep01 GSM205430: met1-3_leaf_fourth-selfed generation_rep02 GSM205432: Col_ leaf_ wildtype_rep01 GSM205435: Col_ leaf_ wildtype_rep02 4: GSE6906 record: Rhythmic growth explained by coincidence between internal and external cues [Arabidopsis thaliana] Summary: Plant hypocotyls elongate in response to darkness. The response to darkness is gated by the circadian clock, such that wild-type plants (Col) only respond to darkness with growth once every 24 hours, whereas arrhythmic lines, such as CCA1-34, will respond to darkness with growth at any time of day. The experiment here was designed to find genes whose expression was correlated with growth. It should also pick up other genes that are gated by the circadian clock or that are direct targets of CCA1. Samples: 12 GSM158680: Col_dark_early_rep1 GSM158681: Col_dark_late_rep1 GSM159273: Col_dark_early_rep2 GSM159291: Col_dark_late_rep2 GSM159298: Col_dark_early_rep3 GSM159299: Col_dark_late_rep3 GSM159300: CCA1-34_dark_early_rep1 GSM159301: CCA1-34_dark_late_rep1 GSM159302: CCA1-34_dark_early_rep2 GSM159304: CCA1-34_dark_late_rep2 GSM159321: CCA1-34_dark_early_rep3 GSM159326: CCA1-34_dark_late_rep3 5: GSE7227 record: microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seeds [Arabidopsis thaliana] Summary: The expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the Col-0, ARF10 and mARF10 sample groups allow the identification of genes regulated by ARF10. Samples: 9 GSM173621: Col-0 rep1 GSM173623: Col-0 rep2 GSM173624: Col-0 rep3 GSM173626: ARF10 rep1 GSM173628: ARF10 rep2 GSM173629: ARF10 rep3 GSM173648: mARF10 rep1 GSM173649: mARF10 rep2 GSM173651: mARF10 rep3 6: GSE7796 record: Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels [Arabidopsis thaliana] Summary: The molecular chaperone HSP90 aids the maturation of a diverse but select set of metastable protein clients, many of which are key to a variety of signal transduction pathways. HSP90 function has been best investigated in animal and fungal systems, where inhibition of the chaperone has exceptionally diverse effects, ranging from reversing oncogenic transformation to facilitating the acquisition of drug resistance. Inhibition of HSP90 in the model plant Arabidopsis thaliana uncovers novel morphologies dependent on normally cryptic genetic variation and increases stochastic variation inherent to developmental processes. The biochemical activity of HSP90 is strictly conserved between animals and plants. However, the substrates and pathways dependent on HSP90 in plants are poorly understood. Samples: 38 GSM189096: HSP90_Reduced_RNAi-B1_Biological_Replicate_1 GSM189097: HSP90_Reduced_RNAi-B1_Biological_Replicate_2 GSM189099: HSP90_Reduced_RNAi-B1_Biological_Replicate_3 GSM189100: HSP90_Reduced_RNAi-C1_Biological_Replicate_1 GSM189101: HSP90_Reduced_RNAi-C1_Biological_Replicate_2 GSM189102: HSP90_Reduced_RNAi-C1_Biological_Replicate_3 GSM189103: HSP90_Reduced_RNAi-A2_Biological_Replicate_1 GSM189104: HSP90_Reduced_RNAi-A2_Biological_Replicate_2 GSM189105: HSP90_Reduced_Control-2_Biological_Replicate_1 GSM189106: HSP90_Reduced_Control-2_Biological_Replicate_2_Technical_Replicate_1 GSM189107: HSP90_Reduced_Control-2_Biological_Replicate_2_Technical_Replicate_2 GSM189108: HSP90_Reduced_RNAi-A1_Biological_Replicate_1 GSM189109: HSP90_Reduced_RNAi-A1_Biological_Replicate_2_Technical_Replicate_1 GSM189110: HSP90_Reduced_RNAi-A1_Biological_Replicate_2_Technical_Replicate_2 GSM189111: HSP90_Reduced_RNAi-A3_Biological_Replicate_1 GSM189112: HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1 GSM189114: HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_2 GSM189116: HSP90_Reduced_Col-0_CS60000_Biological_Replicate_1 GSM189117: HSP90_Reduced_Col-0_CS60000_Biological_Replicate_2 GSM189118: HSP90_Reduced_Col-0_CS60000_Biological_Replicate_3 GSM189119: HSP90_Reduced_Control-1_Biological_Replicate_1 GSM189120: HSP90_Reduced_Control-1_Biological_Replicate_2 GSM189121: HSP90_Reduced_Control-1_Biological_Replicate_3 GSM189122: HSP90_Reduced_Control-3_Biological_Replicate_1 GSM189123: HSP90_Reduced_Control-3_Biological_Replicate_2 GSM189124: HSP90_Reduced_Control-3_Biological_Replicate_3 GSM189163: HSP90_Reduced_hsp90.2-3_Biological_Replicate_1 GSM189164: HSP90_Reduced_hsp90.2-3_Biological_Replicate_2 GSM189165: HSP90_Reduced_hsp90.2-3_Biological_Replicate_3 GSM189170: HSP90_Reduced_Salk_hsp90.3_Biological_Replicate_1 GSM189171: HSP90_Reduced_Salk_hsp90.3_Biological_Replicate_2 GSM189172: HSP90_Reduced_Salk_hsp90.3_Biological_Replicate_3 GSM189173: HSP90_Reduced_Salk_hsp90.2_Biological_Replicate_1 GSM189174: HSP90_Reduced_Salk_hsp90.2_Biological_Replicate_2 GSM189175: HSP90_Reduced_Salk_hsp90.2_Biological_Replicate_3 GSM189176: HSP90_Reduced_Salk_hsp90.1_Biological_Replicate_1 GSM189177: HSP90_Reduced_Salk_hsp90.1_Biological_Replicate_2 GSM189178: HSP90_Reduced_Salk_hsp90.1_Biological_Replicate_3 7: GSE7743 record: Genome-wide gene expression analysis reveals a critical role for CRY1 in the Response of Arabidopsis to High Irradiance [Arabidopsis thaliana] Summary: Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of ELIP1, ELIP2, APX2 and LHCB2.4 in the phyA, phyB, cry1 and cry2 photoreceptor mutants and hy5 and hyh transcription factor mutants. Following exposure to high intensity white light for 3 h (HL, 1000 micro mol quanta m-2 s-1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific mis-regulation of ELIP1/2 and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Samples: 21 GSM187239: Col-O_BL_A GSM187240: Col-O_BL_B GSM187241: Col-O_BL_C GSM187242: Col-O_HL_A GSM187243: Col_HL_B GSM187244: Col-O_HL_C GSM187245: Col-O_LL_A GSM187246: Col-O_LL_B GSM187247: Col-O_LL_C GSM187248: cry1_HL_A GSM187249: cry1_HL_B GSM187250: cry1_HL_C GSM187251: cry1_LL_A GSM187252: cry1_LL_C GSM187253: hy5_HL_A GSM187254: hy5_HL_B GSM187255: hy5_HL_C GSM187256: hy5_LL_A GSM187257: hy5_LL_B GSM187258: hy5_LL_C GSM187418: cry1_LL_B 8: GSE6025 record: eif3h/WT transcript level [Arabidopsis thaliana] Summary: Microarray comparisons of transcript level in wild-type Arabidopsis and eif3h mutant plants. Goal: To detect any change in transcript level between WT and eif3h mutant. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5? leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Samples: 4 GSM139887: eif3h_total_rep1 GSM139894: eif3h_total_rep2 GSM139900: WT_total_rep1 GSM139902: WT_total_rep2 9: GSE6638 record: Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA [Arabidopsis thaliana] Summary: The effect of ahg1 and ahg3 on the gene expression profiles is similar but some genes are differentially affected. Samples: 8 GSM153922: No ABA control rep1 GSM153923: No ABA control rep2 GSM153924: ABA control rep1 GSM153925: ABA control rep2 GSM153926: ahg1-1 rep1 GSM153927: ahg1-1 rep2 GSM153928: ahg3-1 rep1 GSM153929: ahg3-1 rep2 10: GSE6788 record: Expression data of an albino mutant DS 13-2198-1 [Arabidopsis thaliana] Summary: The effect Ds insertion mutation in Ds13-2198-1 line on the gene expression profiles was investigated. The genes for photosynthesis and some transcriptional factors were upregulated while genes for metabolism were downregulated. Samples: 4 GSM156790: control rep1 GSM156791: albino rep1 GSM156792: control rep2 GSM156793: albino rep2 11: GSE6024 record: eif3h/WT polysome loading [Arabidopsis thaliana] Summary: Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant Goal: To find the target mRNAs that are translationally regulated by eIF3h. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5? leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Samples: 8 GSM139880: eif3h_non-polysome_rep1 GSM139884: eif3h_non-polysome_rep2 GSM139885: eif3h_polysome_rep1 GSM139886: eif3h_polysome_rep2 GSM139895: WT_non-polysome_rep1 GSM139897: WT_non-polysome_rep2 GSM139898: WT_polysome_rep1 GSM139899: WT_polysome_rep2 12: GSE7570 record: ATR1_like_Clade_OE_and_miR [Arabidopsis thaliana] Summary: check the effect of over expression and down regulation of this clade of TFs Samples: 19 GSM183504: WT_for_MYB29/76_rep1 GSM183505: WT_for_MYB29/76_rep2 GSM183506: WT_for_MYB29/76_rep3 GSM183507: WT_for_ATR1/MYB51_rep1 GSM183508: WT_for_ATR1/MYB51_rep2 GSM183509: WT_for_miR_rep1 GSM183510: WT_for_miR_rep2 GSM183511: MYB76_OE_rep1 GSM183512: MYB76_OE_rep2 GSM183513: MYB29_OE_rep1 GSM183514: MYB29_OE_rep2 GSM183515: ATR1_OE_rep1 GSM183516: MYB51_OE_rep1 GSM183517: MYB51_OE_rep2 GSM183518: 35S:ATR1_like_miR_rep1 GSM183519: 35S:MYB28_like_miR_rep2 GSM184151: ATR1_OE_rep2 GSM184152: 35S:ATR1_like_miR_rep2 GSM184153: 35S:MYB28_like_miR_rep1 13: GSE7353 record: Early GA response genes in Arabidopsis thaliana [Arabidopsis thaliana] Summary: The phytohormone GA controls multiple important developmental processes in plants such as germination, elongation growth and flowering time. In this experiment, we look for early GA response genes in 7 day-old light-grown Arabidopsis seedlings. To this end we compare four data sets: (1) a GA biosynthesis mutant ga-1 (SALK_109115) mock treated for 1 hr; (2) a GA biosynthesis mutant ga-1 (SALK_109115) treated for 1 hr with 100 µM GA3; (3) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant mock treated for 1 hr; (4) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant treated for 1 hr with 100 µM GA3. In a comparison of the two ga-1 samples, GA regulated genes can be identified, and the assumption is that bona fide GA regulated genes are not responding in the gid1a-1 gid1b-1 gid1c-2 GA receptor mutant. Samples: 12 GSM177119: ga-1 (SALK_109115) mock treated for 1 hr, replicate 1 GSM177120: ga-1 (SALK_109115) mock treated for 1 hr, replicate 2 GSM177121: ga-1 (SALK_109115) mock treated for 1 hr, replicate 3 GSM177122: ga-1 (SALK_109115) treated for 1 hr with 100 uM GA3, replicate 1 GSM177123: ga-1 (SALK_109115) treated for 1 hr with 100 uM GA3, replicate 2 GSM177124: ga-1 (SALK_109115) treated for 1 hr with 100 uM GA3, replicate 3 GSM177125: gid1a-1 gid1b-1 gid1c-2 mock treated for 1 hr, replicate 1 GSM177126: gid1a-1 gid1b-1 gid1c-2 mock treated for 1 hr, replicate 2 GSM177127: gid1a-1 gid1b-1 gid1c-2 mock treated for 1 hr, replicate 3 GSM177128: gid1a-1 gid1b-1 gid1c-2 treated for 1 hr with 100 uM GA3, replicate 1 GSM177129: gid1a-1 gid1b-1 gid1c-2 treated for 1 hr with 100 uM GA3, replicate 2 GSM177130: gid1a-1 gid1b-1 gid1c-2 treated for 1 hr with 100 uM GA3, replicate 3 14: GSE4429 record: Analysis of Arabidopsis thaliana gene expression in response to the bacterial pathogen Pseudomonas syringae ES4326 [Arabidopsis thaliana] Summary: In order to protect themselves from pathogens, plants activate a battery of defense pathways, many of which involve changes in gene expression. We are interested in identifying plant genes that are differentially expressed in response to pathogen exposure, with the ultimate goal of studying the roles of these genes in plant defense. Samples: 2 GSM99793: Col-0_MgSO4_24hpi_C GSM99794: Col-0_PsmES4326_24hpi_C 15: GSE7211 record: A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana [Arabidopsis thaliana] Summary: The oxt6 mutant is an oxidative stress-tolerant Arabidopsis mutant that is deficient in a polyadenylation factor subunit. Expression analysis suggests that impaired poly(A) site choice is responsible for the stress-tolerant phenotype. We used microarrays to understand the link between the polyadenylation defect and stress tolerance. Samples: 10 GSM173442: wild-type Arabidopsis, biological rep1 GSM173443: wild-type Arabidopsis, biological rep2 GSM173444: wild-type Arabidopsis, biological rep3 GSM173445: oxt6 mutant, biological rep1 GSM173446: oxt6 mutant, biological rep2 GSM173447: oxt6 mutant, biological rep3 GSM173448: oxt6:AtCPSF30 line 5, biological rep1 GSM173449: oxt6:AtCPSF30 line 5, biological rep2 GSM173450: oxt6:AtCPSF30 line 6, biological rep1 GSM173451: oxt6:AtCPSF30 line 6, biological rep2 16: GSE7112 record: Abscisic acid effect on wild type and the abh1 mutant [Arabidopsis thaliana] Summary: Analysis of the abh1 mutant Arabidopsis plants following treatment with 50 uM abscisic acid (ABA). ABH1 encodes the large (80kDa) subunit of the nuclear mRNA cap binding complex and affects early ABA signal transduction events (Hugouvieux et al., 2001, Cell 106, 477). Samples: 8 GSM170896: Col-0 -ABA repl1 GSM170897: Col-0 +ABA repl1 GSM170899: abh1 -ABA repl1 GSM170911: abh1 +ABA repl1 GSM170923: Col-0 -ABA repl2 GSM170930: abh1 -ABA repl2 GSM170931: Col-0 +ABA repl2 GSM170940: abh1 +ABA repl2 17: GSE5747 record: Genome-wide cell cycle studies [Arabidopsis thaliana] Summary: This experiment was provided by TAIR (http://arabidopsis.org). Effective analysis of gene expression during the cell cycle depends on achieving a good level of synchronisation. Until recently, analysis of cell cycle processes in plants has been hampered by the lack of synchronizable cell suspensions for Arabidopsis. We have recently developed a cell synchrony system for Arabidopsis cell suspensions MM1 and MM2d, and have developed two methods of synchronization. The first synchronizes cycling cells by blocking cells at the G1/S boundary using aphidicolin. The second uses sucrose removal and resupply to synchronize cells during re-entry into the cell cycle. Cell cycle synchrony in suspension cultured cells: cells can be reproducibly synchronized by blocking at the G1/S boundary or in early S phase using aphidicolin for 24 hr and then reversing the block by washing (Menges and Murray, 2002). Samples: 10 GSM133945: Murray_2-1_T0-APH_Rep1_ATH1 GSM133946: Murray_2-2_T2-APH_Rep1_ATH1 GSM133947: Murray_2-3_T4-APH_Rep1_ATH1 GSM133948: Murray_2-4_T6-APH_Rep1_ATH1 GSM133949: Murray_2-5_T8-APH_Rep1_ATH1 GSM133950: Murray_2-6_T10-APH_Rep1_ATH1 GSM133951: Murray_2-7_T12-APH_Rep1_ATH1 GSM133952: Murray_2-8_T14-APH_Rep1_ATH1 GSM133953: Murray_2-9_T16-APH_Rep1_ATH1 GSM133954: Murray_2-10_T19-APH_Rep1_ATH1 18: GSE5617 record: AtGenExpress: Light treatments [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC). The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 48 GSM131169: AtGen_D-1_1-DL_REP1_ATH1 GSM131170: AtGen_D-2_1-FL_REP1_ATH1 GSM131171: AtGen_D-3_1-PL_REP1_ATH1 GSM131172: AtGen_D-4_1-RL_REP1_ATH1 GSM131173: AtGen_D-5_1-BL_REP1_ATH1 GSM131174: AtGen_D-6_1-AL_REP1_ATH1 GSM131175: AtGen_D-7_1-UL_REP1_ATH1 GSM131176: AtGen_D-8_1-WL_REP1_ATH1 GSM131177: AtGen_D-9_1-DS_REP1_ATH1 GSM131178: AtGen_D-10_1-FS_REP1_ATH1 GSM131179: AtGen_D-11_1-PS_REP1_ATH1 GSM131180: AtGen_D-12_1-RS_REP1_ATH1 GSM131181: AtGen_D-13_1-BS_REP1_ATH1 GSM131182: AtGen_D-14_1-AS_REP1_ATH1 GSM131183: AtGen_D-15_1-US_REP1_ATH1 GSM131184: AtGen_D-16_1-WS_REP1_ATH1 GSM131185: AtGen_D-18_2-FL_REP2_ATH1 GSM131186: AtGen_D-19_2-PL_REP2_ATH1 GSM131187: AtGen_D-20_2-RL_REP2_ATH1 GSM131188: AtGen_D-21_2-BL_REP2_ATH1 GSM131189: AtGen_D-22_2-AL_REP2_ATH1 GSM131190: AtGen_D-23_2-UL_REP2_ATH1 GSM131191: AtGen_D-24_2-WL_REP2_ATH1 GSM131192: AtGen_D-25_2-DS_REP2_ATH1 GSM131193: AtGen_D-27_2-PS_REP2_ATH1 GSM131194: AtGen_D-28_2-RS_REP2_ATH1 GSM131195: AtGen_D-29_2-BS_REP2_ATH1 GSM131196: AtGen_D-30_2-AS_REP2_ATH1 GSM131197: AtGen_D-31_2-US_REP2_ATH1 GSM131198: AtGen_D-32_2-WS_REP2_ATH1 GSM131199: AtGen_D-33_3-DL_REP3_ATH1 GSM131200: AtGen_D-34_3-FL_REP3_ATH1 GSM131201: AtGen_D-35_3-PL_REP3_ATH1 GSM131202: AtGen_D-36_3-RL_REP3_ATH1 GSM131203: AtGen_D-37_3-BL_REP3_ATH1 GSM131204: AtGen_D-38_3-AL_REP3_ATH1 GSM131205: AtGen_D-39_3-UL_REP3_ATH1 GSM131206: AtGen_D-40_3-WL_REP3_ATH1 GSM131207: AtGen_D-41_3-DS_REP3_ATH1 GSM131208: AtGen_D-42_3-FS_REP3_ATH1 GSM131209: AtGen_D-43_3-PS_REP3_ATH1 GSM131210: AtGen_D-44_3-RS_REP3_ATH1 GSM131211: AtGen_D-45_3-BS_REP3_ATH1 GSM131212: AtGen_D-46_3-AS_REP3_ATH1 GSM131213: AtGen_D-47_3-US_REP3_ATH1 GSM131214: AtGen_D-48_3-WS_REP3_ATH1 GSM131215: AtGen_D-17_2-DL_REP2_ATH1 GSM131216: AtGen_D-26_1-FS_REP2_ATH1 19: GSE6178 record: Mechanisms of DNA double strand break repair in Arabidopsis non-homologous end joining mutants [Arabidopsis thaliana] Summary: The proposal aims to characterise the pathways of DSB repair and recombination in Arabidopsis with the main focus of this research being the NHEJ pathway of illegitimate recombination. We will build on our expertise and resources in the field of DSB repair in plants, using the Arabidopsis NHEJ mutant atku80 which is an excellent model system for the study of DSB repair in higher eukaryotes (West et al., 2002 Plant J. 31, 517-28). Comparison of the transcriptome in NHEJ mutant and wild type plants under different experimental conditions will identify novel candidate genes involved in DNA DSB repair or damage signalling pathways.We will conduct 4 separate experiments on Arabidopsis seedlings grown on 0.5 MS media: the first will be a control consisting of Wassilewskija (WS-2) plants grown under standard conditions. Samples: 4 GSM142882: CW001_ATH1_A1.1-WestC-wsu GSM142883: CW001_ATH1_A1.2-WestC-wsb GSM142884: CW001_ATH1_A1.3-WestC-kuu GSM142885: CW001_ATH1_A1.4-WestC-kub 20: GSE6176 record: Impact of Type III effectors on plant defense responses [Arabidopsis thaliana] Summary: Our interest lies in how plants respond to bacterial pathogens. Over the past three years we have identified and documented reproducible, landmark biochemical and molecular events following the challenge of Arabidopsis with the phytopathogenic enterobacteria P. syringae. Significantly, our studies revealed 60% of cDNA-AFLP differentials not present on the 8,200 feature GeneChips and 20% absent from public EST databases (de Torres in press). We now seek to exploit this background using carefully defined time-points to analyse global changes in the Arabidopsis transcriptome using challenges selected to define gene targets implicated in (i) expression of basal immunity (ii) the establishment of successful parasitism (resistance) by a virulent pathogen (host). The results will provide a rationale for future functional assays of the identified pathways using transgenic knockouts and mutant analyses. Samples: 27 GSM142829: GM001_ATH1_A11-Torres-5N3 GSM142830: GM001_ATH1_A14-Torres-4N3_repeat2 GSM142831: GM001_ATH1_A30-Torres-9N6_repeat1 GSM142832: GM001_ATH1_A9-Torres-3N6_repeat2 GSM142833: MG001_ATH1_A10-Torres-5N1 GSM142834: MG001_ATH1_A12-Torres-5N6 GSM142835: MG001_ATH1_A13-Torres-4N1 GSM142836: MG001_ATH1_A15-Torres-4N6 GSM142837: MG001_ATH1_A16-Torres-6N1 GSM142838: MG001_ATH1_A17-Torres-6N3 GSM142839: MG001_ATH1_A18-Torres-6N6 GSM142840: MG001_ATH1_A1-Torres-1N1 GSM142841: MG001_ATH1_A22-Torres-7N1 GSM142842: MG001_ATH1_A23-Torres-7N3 GSM142843: MG001_ATH1_A24-Torres-7N6 GSM142844: MG001_ATH1_A25-Torres-8N1 GSM142845: MG001_ATH1_A26-Torres-8N3 GSM142846: MG001_ATH1_A27-Torres-9N1 GSM142847: MG001_ATH1_A28-Torres-9N1 GSM142848: MG001_ATH1_A29-Torres-9N3 GSM142849: MG001_ATH1_A2-Torres-1N3 GSM142850: MG001_ATH1_A3-Torres-1N6 GSM142851: MG001_ATH1_A4-Torres-2N1 GSM142852: MG001_ATH1_A5-Torres-2N3 GSM142853: MG001_ATH1_A6-Torres-2N6 GSM142854: MG001_ATH1_A7-Torres-3N1 GSM142855: MG001_ATH1_A8-Torres-3N3 21: GSE6171 record: Comparative transcriptome analysis between wild-type and gpa1 mutant in response to ABA [Arabidopsis thaliana] Summary: Mutations in the heterotrimeric G-protein a-subunit of Arabidopsis, GPA1, leads to deficiency in ABA-induced stomatal closure (Wang et al., 2001). To further investigate whether GPA1 is involved in the regulation of gene expression in response to ABA, we examined the induction of known ABA-inducible genes in the gpa1 mutant and compared it to wild-type. We found significant differences in levels of ABA-induced expression between wild-type and gpa1 mutant. In order to systematically investigate GPA1 involvement in ABA signalling leading to gene expression, we are requesting the transcriptome analysis of the gpa1 mutant in response to ABA.In detail, 2 week old wild-type and gpa1 plants grown in the 16/8 hrs light and dark cycle will be treated with either ABA or with a control solution for 3 hours. Samples: 4 GSM142784: HO001_ATH1_A1-Okamo-gpal-ABA GSM142785: HO001_ATH1_A2-Okamo-gpal-control GSM142786: HO001_ATH1_A3-Okamo-WS-ABA GSM142787: HO001_ATH1_A4-Okamo-WS-control 22: GSE6169 record: Seedling transcriptome affected by a far-red light preconditioning treatment to block chloroplast development. [Arabidopsis thaliana] Summary: This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. Samples: 10 GSM142772: AM002_ATH1_A7-MCCOR-GFB GSM142773: AM002_ATH1_A8-MCCOR-GDB GSM142774: AM002_ATH1_A9-MCCOR-AFA GSM142775: AM002_ATH1_A10-MCCOR-ADA GSM142776: AM002_ATH1_A1-MCCOR-WFA GSM142777: AM002_ATH1_A2-MCCOR-WDA GSM142778: AM002_ATH1_A3-MCCOR-GFA GSM142779: AM002_ATH1_A4-MCCOR-GDA GSM142780: AM002_ATH1_A5-MCCOR-WFB GSM142781: AM002_ATH1_A6-MCCOR-WDB 23: GSE6167 record: The molecular basis of chilling and freezing stress [Arabidopsis thaliana] Summary: Our analysis of the sfr6 freezing-sensitive mutant (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.) and cls8 (unpublished) chilling-sensitive mutant of Arabidopsis, has revealed that the expression of certain cold-regulated genes is aberrant in both these mutants. In order to understand the molecular basis of chilling and freezing stress in Arabidopsis and also to determine commonalities and differences between these 2 different physiological stress-tolerance processes, we request transcriptome analysis for both of these mutants compared to wild type in one experiment, upon cold treatment and at ambient conditions. The sfr6 mutant shows the most severe phenotype with respect to cold gene expression, but is tolerant to chilling (Knight, H., Veale, E., Warren, G. Samples: 6 GSM142764: MK001_ATH1_A1.1-Knigh-wam GSM142765: MK001_ATH1_A1.2-Knigh-wco GSM142766: MK001_ATH1_A1.3-Knigh-sam GSM142767: MK001_ATH1_A1.4-Knigh-sco GSM142768: MK001_ATH1_A1.5-Knigh-cam-repeat GSM142769: MK001_ATH1_A-1.6-Knight-cco_repeat2 24: GSE6830 record: Group II-A WRKY transcription factors and early leaf senescence (2) [Arabidopsis thaliana] Summary: In our laboratory we are interested in studying the functions of WRKY zink finger type transcription factors. There are 74 members of this gene family in Arabidopsis. WRKY factors are key regulators of distinct plant defense responses and are involved in certain developmental programs e.g. plant senescence. We would like to determine the functions of a small sub-group (group II-a) of WRKY factors. Our aim to compare and contrast the gene expression profiles of 35 days-old untreated wild type and WRKY T-DNA knockout plants grown in a growth chamber under long day growth conditions. All plants chosen at this stage showed slight yellowing of the first two to four leaves. Experimenter name: Bekir Uelker Experimenter phone: 49-221-5062-310 Experimenter fax: 49-221-5062-353 Experimenter depa. Samples: 8 GSM157365: Ulker_1-1_WT-Col-0-L_Rep1_ATH1 GSM157366: Ulker_1-2_WRKY-KO-02_Rep1_ATH1 GSM157367: Ulker_1-3_WRKY-KO-07_Rep1_ATH1 GSM157368: Ulker_1-4_WRKY-KO-54_Rep1_ATH1 GSM157369: Ulker_1-5_WRKY-KO-40_Rep1_ATH1 GSM157370: Ulker_1-6_WRKY-KO-30_Rep1_ATH1 GSM157371: Ulker_1-7_WRKY-KO-56_Rep1_ATH1 GSM157372: Ulker_1-8_WT_Col-0-S_Rep1_ATH1 25: GSE6828 record: Transcriptome response to change in ploidy level in Arabidopsis [Arabidopsis thaliana] Summary: By reciprocally crossing 2x and 4x C24 ecotype plants, we have generated 4 types of offspring with various ploidy (2x; 3x; 4x) or parent-of-origin genome dosage (3x from 4xper2x; 3x from 2xper4x). For each offspring generated, total RNA was extracted using Trizol from 8 seedlings 9 days after germination (developmental stage1.02, 2 leaves). Sample names: DIP diploid TET tetraploid TFE triploid female excess TME triplod male excess Experimenter name: Olivier Garnier Experimenter phone: 00-353-21-490-4028 Experimenter address: Plant molecular genetics lab, Dpt of Biochemistry, UCC Experimenter address: Lee Maltings Prospect row Experimenter zip/postal_code: Cork Experimenter country: Ireland Samples: 11 GSM157347: Garnier_1-1_C24-DIP_Rep1_ATH1 GSM157348: Garnier_1-2_C24-DIP_Rep2_ATH1 GSM157349: Garnier_1-4_C24-TFE_Rep1_ATH1 GSM157350: Garnier_1-5_C24-TFE_Rep2_ATH1 GSM157351: Garnier_1-6_C24-TFE_Rep3_ATH1 GSM157352: Garnier_1-7_C24-TME_Rep1_ATH1 GSM157353: Garnier_1-8_C24-TME_Rep2_ATH1 GSM157354: Garnier_1-9_C24-TME_Rep3_ATH1 GSM157355: Garnier_1-10_C24-TET_Rep1_ATH1 GSM157356: Garnier_1-11_C24-TET_Rep2_ATH1 GSM157357: Garnier_1-12_C24-TET_Rep3_ATH1 26: GSE6162 record: Transcriptome analysis of Arabidopsis microgametogenesis [Arabidopsis thaliana] Summary: Aims We aim to use transcriptome analysis to establish on a genome-wide scale the identity and regulatory clusters of genes that specify microgametogenesis from the haploid microspore to mature functional pollen in Arabidopsis. Background Pollen as the haploid male gametophyte plays a vital role in plant fertility and crop production through the ability to deliver the male gametes in fertilisation. Despite the obvious importance for plant fertility and crop production we have a very limited understanding of the regulatory mechanisms that have evolved to specify male gametophyte development and functions and less than 150 genes have been identified that are gametophytically expressed in the anther.The availability of functional genomic resources now provides the opportunity to undertake a comprehensive approach to describing cellular development in terms of the transcriptome. Samples: 7 GSM142734: DH001_ATH1_A1-UNM1 GSM142735: DH001_ATH1_A2-BCP1 GSM142736: DH001_ATH1_A3-TCP1 GSM142737: DH001_ATH1_A4-UNM2 GSM142738: DH001_ATH1_A5-BCP2 GSM142739: DH001_ATH1_A6-TCP2 GSM142740: DH001_ATH1_A7-MPG1 27: GSE6153 record: Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis [Arabidopsis thaliana] Summary: Arabidopsis, when grown under short day conditions (16 hours dark, 8 hours light, 22oC) develop extensive secondary thickened hypocotyls with both a vascular and cork cambium (Chaffey et al, 2002, Phys. Plant., 114:594-600). It has been found that once secondary xylem development is completed within the Arabidopsis hypocotyls, it closely resembles the structure of the wood of angiosperm trees (Chaffey et al, 2002, Phys. Plant., 114:594-600). We can utilise this model Arabidopsis tree to identify genes that are important for secondary cell wall formation in xylem cells and therefore important for wood development. Columbia plants were grown for 3 months under short day conditions and secondary thickened hypocotyls were snap-frozen in liquid nitrogen. RNA was isolated from these hypocotyl. Samples: 2 GSM142661: MB002_ATH1_A1-Eland-ch1 GSM142662: MB002_ATH1_A2-Eland-ch2 28: GSE6151 record: The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis [Arabidopsis thaliana] Summary: Plants that exhibit secondary growth, such as trees, are a prominent feature of terrestrial ecosystems. Furtherecondary growth itself, particularly wood, has huge economic value. Despite the importance of secondary growth from both basic and applied science perspectives, little is known about the molecular mechanisms that underpin this facet of plant development. The proposed microarray experiments are designed to expand our knowledge of the regulation of secondary growth by combining the power of Arabidopsis genetics with complete transcriptome analysis. It is now well established that Arabidopsis can be grown under conditions that induce secondary growth in the hypocotyl, albeit small, wood. We have grown 8500 Arabidopsis plants of different genotypes under these conditions and will extract RNA from the developing vascular cambia of these plants to subject them to complete transcriptome analysis.The mutants that we have chosen for these analyses are all related to each other on the basis of the fact that they impact dormancy in either seeds or shoots (abi1, aba1, max4, axr1, AtMYB61 knockout, AtMYB50 knockout). Samples: 36 GSM142623: MC002_ATH1_A1.1-dubos-wtx GSM142624: MC002_ATH1_A1.2-dubos-wtx GSM142625: MC002_ATH1_A1.3-dubos-wtx GSM142626: MC002_ATH1_A2.1-dubos-wtc GSM142627: MC002_ATH1_A2.2-dubos-wtc GSM142628: MC002_ATH1_A2.3-dubos-wtc GSM142629: MC002_ATH1_A3.1-dubos-6kx GSM142630: MC002_ATH1_A3.2-dubos-6kx GSM142631: MC002_ATH1_A3.3-dubos-6kx GSM142632: MC002_ATH1_A4.1-dubos-6kc GSM142633: MC002_ATH1_A4.2-dubos-6kc GSM142634: MC002_ATH1_A4.3-dubos-6kc GSM142635: MC002_ATH1_A5.1-dubos-5kx GSM142636: MC002_ATH1_A5.2-dubos-5kx GSM142637: MC002_ATH1_A5.3-dubos-5kx GSM142638: MC002_ATH1_A6.1-dubos-5kc_repeat GSM142639: MC002_ATH1_A6.2-dubos-5kc GSM142640: MC002_ATH1_A6.3-dubos-5kc GSM142641: MC002_ATH1_A7.1-dubos-wLh GSM142642: MC002_ATH1_A7.2-dubos-wLh GSM142643: MC002_ATH1_A7.3-dubos-wLh GSM142644: MC002_ATH1_A8.1-dubos-aih GSM142645: MC002_ATH1_A8.2-dubos-aih GSM142646: MC002_ATH1_A8.3-dubos-aih GSM142647: MC002_ATH1_A9.1-dubos-aah GSM142648: MC002_ATH1_A9.2-dubos-aah GSM142649: MC002_ATH1_A9.3-dubos-aah GSM142650: MC002_ATH1_A10.1-dubos-wth GSM142651: MC002_ATH1_A10.2-dubos-wth GSM142652: MC002_ATH1_A10.3-dubos-wth GSM142653: MC002_ATH1_A11.1-dubos-mxh GSM142654: MC002_ATH1_A11.2-dubos-mxh GSM142655: MC002_ATH1_A11.3-dubos-mxh GSM142656: MC002_ATH1_A12.1-dubos-arh GSM142657: MC002_ATH1_A12.2-dubos-arh GSM142658: MC002_ATH1_A12.3-dubos-arh 29: GSE6154 record: Molecular basis of respiratory burst-mediated thermotolerance in Arabidopsis [Arabidopsis thaliana] Summary: We have been determining signalling components essential for heat tolerance in Arabidopsis thaliana (Larkindale, J., and Knight, M.R. (2002). Protection against heat stress-induced oxidative damage in Arabidopsis involves calcium, abscisic acid, ethylene, and salicylic acid. Plant Physiol 128, 682-695). We have most recently found that a heat-induced respiratory burst is necessary for tolerance to high temperatures in Arabidopsis (Larkindale, Torres, Jones and Knight, unpublished). We have observed that one of the Arabidopsis respiratory burst homologues, AtrbohB, is necessary for the generation of this AOS burst in response to heat, and consequently we have also found that an AtrbohB null mutant shows reduced tolerance to heating (Larkindale, Torres, Jones and Knight, unpublished). This mutant also shows reduced expression of genes from the HSP90 family (Evans, Larkindale and Knight, unpublished).This application is for transcriptomic analysis of the AtrbohB null mutant in response to heat, in order to understand which genes are activated as a result of heat-induced respiratory bursts in Arabidopsis and also which genes are necessary for physiological thermotolerance in Arabidopsis. Samples: 6 GSM142663: NE001_ATH1_A1-Evans-w20 GSM142664: NE001_ATH1_A2-Evans-w30 GSM142665: NE001_ATH1_A3-Evans-w40 GSM142666: NE001_ATH1_A4-Evans-m20 GSM142667: NE001_ATH1_A5-Evans-m30 GSM142668: NE001_ATH1_A6-Evans-m40-repeat 30: GSE6831 record: Systemic response to avirulent bacterial infection [Arabidopsis thaliana] Summary: In the absence of adaptive immunity displayed by animals, plants respond locally to biotic challenge via inducible basal defense networks activated through recognition and response toconserved pathogen associated molecular patterns (PAMPs). In addition, immunity can be induced in tissues remote from infection sites via systemic acquired resistance (SAR), initiated following gene-for-gene recognition between plant resistance proteins and microbial effectors.The nature of the mobile signal and remotely activated networks responsible for establishing SAR remain unclear. Here we show that despite the absence of PAMP contact, systemically responding leaves rapidly activate a SAR transcriptional signature with strong similarity to local basal defense. Jasmonates have previously been implicated in systemic signalling in response to wounding and plant herbivory but not SAR. Samples: 9 GSM157373: Truman_1-1_Pst-DC3000-4hpi_Rep1_ATH1 GSM157374: Truman_1-2_Pst-DC3000(hrpA)-4hpi_Rep1_ATH1 GSM157375: Truman_1-3_Pst-DC3000(avrRpm1)-4hpi_Rep1_ATH1 GSM157376: Truman_1-4_Pst-DC3000-4hpi_Rep2_ATH1 GSM157377: Truman_1-5_Pst-DC3000(hrpA)-4hpi_Rep2_ATH1 GSM157378: Truman_1-6_Pst-DC3000(avrRpm1)-4hpi_Rep2_ATH1 GSM157379: Truman_1-7_Pst-DC3000-4hpi_Rep3_ATH1 GSM157380: Truman_1-8_Pst-DC3000(hrpA)-4hpi_Rep3_ATH1 GSM157381: Truman_1-9_Pst-DC3000(avrRpm1)-4hpi_Rep3_ATH1 31: GSE6829 record: Group II-A WRKY transcription factors and early leaf senescence [Arabidopsis thaliana] Summary: In our laboratory we are interested in studying the functions of WRKY zinc finger type transcription factors. There are 74 members of this gene family in Arabidopsis. WRKY factors are key regulators of distinct plant defense responses and are involved in certain developmental programs e.g. trichome development and plant leaf senescence. We would like to determine the functions of a small sub-group (group II-a) of WRKY factors in response to bacterial infection. Our aim is to compare and contrast the gene expression profiles of 3-week-old wild type and WRKY T-DNA knockout mutants grown in a growth chamber under long day growth conditions and subsequently challenged for 6 hours with the virulent bacterial pathogen /Pseudomonas syringae/ DC3000. Experimenter name: Bekir Uelker Experimenter ph. Samples: 7 GSM157358: Ulker_2-1_WT-Col-0-L-MgCl2_Rep1_ATH1 GSM157359: Ulker_2-2_WRKY-KO-02-Pst-DC3000_Rep1_ATH1 GSM157360: Ulker_2-3_WRKY-KO-07-Pst-DC3000_Rep1_ATH1 GSM157361: Ulker_2-4_WRKY-KO-30-Pst-DC3000_Rep1_ATH1 GSM157362: Ulker_2-5_WRKY-KO-40-Pst-DC3000_Rep1_ATH1 GSM157363: Ulker_2-6_WRKY-KO-13-Pst-DC3000_Rep1_ATH1 GSM157364: Ulker_2-7_WT-Col-0-L-Pst-DC3000_Rep1_ATH1 32: GSE6161 record: Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4. [Arabidopsis thaliana] Summary: Background: Release of the caesium radioisotope 137Cs during weapons testing and industrial activity has contaminated thousands of hectares of agricultural land. Ingesting 137Cs has damaging and, sometimes, fatal effects. Most Cs enters the food chain through plants. The generation of _safe_ crops that exclude Cs and can be cultivated on contaminated land requires knowledge about the mechanisms for Cs uptake. Caesium is chemically similar to potassium (K) and might enter plants through K+ transporters in the plasma membrane of root cells. To determine which transporters mediate Cs entry to plants, we have compared the accumulation of Cs and K by wildtype Arabidopsis with mutants lacking specific K+ transporters. Preliminary results showed that Cs concentration in the shoots of akt1-1, cngc1 and cngc4 (obtained from the Wisconsin T-DNA knockout facility) differed significantly from the Wassilewskija wildtype (Ws-2). Samples: 12 GSM142721: CH001_ATH1_A001-Hampt-wsa GSM142723: CH001_ATH1_A002-Hampt-aka GSM142724: CH001_ATH1_A003-Hampt-c4a_repeat GSM142725: CH001_ATH1_A004-Hampt-c1a GSM142726: CH001_ATH1_A005-Hampt-wsb_repeat GSM142727: CH001_ATH1_A006-Hampt-akb GSM142728: CH001_ATH1_A007-Hampt-c4b GSM142729: CH001_ATH1_A008-Hampt-c1b GSM142730: CH001_ATH1_A009-Hampt-wsc_repeat GSM142731: CH001_ATH1_A010-Hampt-akc GSM142732: CH001_ATH1_A011-Hampt-c4c GSM142733: CH001_ATH1_A012-Hampt-c1c 33: GSE6179 record: An investigation into transcriptional changes in developing Arabidopsis leaf caused by novel signalling protein, SPH1. [Arabidopsis thaliana] Summary: Arabidopsis genome sequencing has revealed the presence of at least three extensive gene families that may encode protein ligands. One of these, the SPH (S-protein homologue) family, was identified as a direct result of our studies on self-incompatibility in Papaver. The Arabidopsis SPH gene family consists of 81 members. We have initiated experimental work on a subset of these. RT-PCR studies indicate that many, if not all, SPH genes are expressed. Each SPH gene encodes an N-terminal signal peptide sequence and thus SPH proteins are likely to be secreted. Until recently none of the genes in this family had known function. However we have evidence that one member of the family, SPH1 is involved in leaf vascular development. In order to determine the function of SPH1, Arabidopsis plants were transformed with an SPH1 antisense construct. Samples: 12 GSM142886: MW001_ATH1_A1-Wheel-a05 GSM142887: MW001_ATH1_A1-Wheel-a14 GSM142888: MW001_ATH1_A1-Wheel-w05 GSM142889: MW001_ATH1_A1-Wheel-w14 GSM142890: MW001_ATH1_A2-Wheel-a05 GSM142891: MW001_ATH1_A2-Wheel-a14_repeat GSM142892: MW001_ATH1_A2-Wheel-w05 GSM142893: MW001_ATH1_A2-Wheel-w14 GSM142894: MW001_ATH1_A3-Wheel-a05 GSM142895: MW001_ATH1_A3-Wheel-a14_repeat GSM142896: MW001_ATH1_A3-Wheel-w05 GSM142897: MW001_ATH1_A3-Wheel-w14 34: GSE6177 record: The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress responses [Arabidopsis thaliana] Summary: Our goals are to discover the basis of the stress-sensitive phenotypes of the sfr2, sfr3 and sfr6 mutants, and to distinguish damage-repair from damage-prevention-related transcription in the wild type. The effects of sfr2 and sfr3 on cold-induced gene expression will be observed. Since sfr6 causes sensitivity to drought as well as freezing, the effects of sfr6 on the transcriptional response to drought is studied; an observation of cold-induced sfr6 expression is needed for direct comparison to the effect of drought. Unstressed mutants, and equivalently-stressed wild types, are necessary controls. The above experiments are conducted on tissue-culture-grown plants grown under 24 hr illumination for maximum reproducibility and comparability to other transcriptomic experiments.Freezing causes physiological changes even in a hardy, cold-acclimated wild type. Samples: 26 GSM142856: GW001_ATH1_A1-Warre-Wna_repeat1 GSM142857: GW001_ATH1_A2-Warre-Wna GSM142858: GW001_ATH1_A3-Warre-6na GSM142859: GW001_ATH1_A4-Warre-6na GSM142860: GW001_ATH1_A5-Warre-3na GSM142861: GW001_ATH1_A6-Warre-3na GSM142862: GW001_ATH1_A7-Warre-2na GSM142863: GW001_ATH1_A8-Warre-2na GSM142864: GW001_ATH1_A9-Warre-Wca GSM142865: GW001_ATH1_A10-Warre-Wca GSM142866: GW001_ATH1_A11-Warre-6ca GSM142867: GW001_ATH1_A12-Warre-6ca GSM142868: GW001_ATH1_A13-Warre-3ca GSM142869: GW001_ATH1_A14-Warre-3ca GSM142870: GW001_ATH1_A15-Warre-2ca GSM142871: GW001_ATH1_A16-Warre-2ca GSM142872: GW001_ATH1_A17-Warre-Wdr GSM142873: GW001_ATH1_A18-Warre-Wdr GSM142874: GW001_ATH1_A19-Warre-6dr GSM142875: GW001_ATH1_A20-Warre-6dr_repeat1 GSM142876: GW001_ATH1_A21-Warre-00f GSM142877: GW001_ATH1_A22-Warre-00f GSM142878: GW001_ATH1_A23-Warre-03f GSM142879: GW001_ATH1_A24-Warre-03f GSM142880: GW001_ATH1_A25-Warre-24f GSM142881: GW001_ATH1_A26-Warre-24f 35: GSE6827 record: Comparison of transcriptional profiles between sni1 and wild type [Arabidopsis thaliana] Summary: Microarray experiment was performed using 4-week old plants to compare transcriptional profiles between sni1 (suppressor of npr1) and wild type (Col-0). Three biological replicates were included. Experimenter name: Wendy Durrant Experimenter phone: 1(919)613-8175 Experimenter fax: 1(919)613-8177 Experimenter department: Durrant Lab Experimenter institute: Duke University Experimenter address: Rm. B354, LSRC Bldg. Experimenter address: Research Dr. Experimenter address: Duke University Experimenter address: Durham, NC Experimenter zip/postal_code: 27708 Experimenter country: USA Samples: 6 GSM157341: Durrant_1-1_wild-type_Rep1_ATH1 GSM157342: Durrant_1-2_wild-type_Rep2_ATH1 GSM157343: Durrant_1-3_wild-type_Rep3_ATH1 GSM157344: Durrant_1-4_sni1_Rep1_ATH1 GSM157345: Durrant_1-5_sni1_Rep2_ATH1 GSM157346: Durrant_1-6_sni1_Rep3_ATH1 36: GSE6826 record: Identification of candidate Arabidillo target genes in Arabidopsis [Arabidopsis thaliana] Summary: Arabidopsis has two genes, Arabidillo-1 and -2, related to animal Armadillo/ beta-catenin (Coates, 2003). Armadillo/beta-catenin directly activates the expression of developmental and cell proliferation genes, and also independently regulates cell-cell adhesion. Arabidillo proteins are nuclear and promote lateral root development. We aim to identify candidate Arabidillo target genes by comparing the transcriptomes of wild type, arabidillo-1/2 mutant and Arabidillo-1 overexpressing lines. The experiment will compare Col-0 (3 slides) with a 35S::Arabidillo-1-YFP overexpressing line (3 slides) and Col-3 with the arabidillo-1/2 mutant (3 slides). Each RNA prep will be from plate-grown 7-day old seedlings. Reference: Coates, JC (2003) Armadillo repeat proteins: beyond the animal kingdom? Tr. Samples: 12 GSM157329: Coates_1-1_Col-0_Rep1_ATH1 GSM157330: Coates_1-2_ara1OX_Rep1_ATH1 GSM157331: Coates_1-3_Col-3_Rep1_ATH1 GSM157332: Coates_1-4_ara1/2mut_Rep1_ATH1 GSM157333: Coates_1-5_Col-0_Rep2_ATH1 GSM157334: Coates_1-6_ara1OX_Rep2_ATH1 GSM157335: Coates_1-7_Col-3_Rep2_ATH1 GSM157336: Coates_1-8_ara1/2mut_Rep2_ATH1 GSM157337: Coates_1-9_Col-0_Rep3_ATH1 GSM157338: Coates_1-10_ara1OX_Rep3_ATH1 GSM157339: Coates_1-11_Col-3_Rep3_ATH1 GSM157340: Coates_1-12_ara1/2mut_Rep3_ATH1 37: GSE6825 record: Differential gene expression patterns in potassium-starved and Caesium-treated plants [Arabidopsis thaliana] Summary: At high concentrations ceasium (Cs) is toxic to plant growth. This toxic effect may occur when Cs blocks potassium (K) uptake mechanisms in plants. Consequently, plants starved of K and plants exposed to toxic concentrations of Cs should have similar gene expression patterns. To test this hypothesis, Arabidopsis will initially be grown on agar containing 1/10 MS salts before being transferred to either 1/10 MS nutrient solution (control plants), 1/10 MS nutrient solution containing 2 mM Cs, or 1/10 MS nutrient solution with no K. Roots and shoot will then be harvested seven days after transfer and used to challenge ATH1 GeneChips. Experimenter name: John Hammond Experimenter phone: 01789 470382 Experimenter fax: 01789 470552 Experimenter institute: Warwick University Experimenter address: . Samples: 18 GSM157311: Hammond_3-1_Control-shoot_Rep1_ATH1 GSM157312: Hammond_3-2_Potassium-starved-shoot_Rep1_ATH1 GSM157313: Hammond_3-3_Caesium-treated-shoot_Rep1_ATH1 GSM157314: Hammond_3-4_Control-root_Rep1_ATH1 GSM157315: Hammond_3-5_Potassium-starved-root_Rep1_ATH1 GSM157316: Hammond_3-6_Caesium-treated-root_Rep1_ATH1 GSM157317: Hammond_3-7_Control-shoot_Rep2_ATH1 GSM157318: Hammond_3-8_Potassium-starved-shoot_Rep2_ATH1 GSM157319: Hammond_3-9_Caesium-treated-shoot_Rep2_ATH1 GSM157320: Hammond_3-13_Control-shoot_Rep3_ATH1 GSM157321: Hammond_3-14_Potassium-starved-shoot_Rep3_ATH1 GSM157322: Hammond_3-15_Caesium-treated-shoot_Rep3_ATH1 GSM157323: Hammond_3-16_Control-root_Rep3_ATH1 GSM157324: Hammond_3-17_Potassium-starved-root_Rep3_ATH1 GSM157325: Hammond_3-18_Caesium-treated-root_Rep3_ATH1 GSM157326: Hammond_3-10_Control-root_Rep2_ATH1 GSM157327: Hammond_3-11_Potassium-starved-root_Rep2_ATH1 GSM157328: Hammond_3-12_Caesium-treated-root_Rep2_ATH1 38: GSE6824 record: Identification of genes involved in nutritional regulation of root architecture [Arabidopsis thaliana] Summary: AIM: 1. To identify genes that respond to N-deficiency and N-resupply and 2. To identify the subset of these genes that are under the (direct or indirect) regulatory influence of the ANR1 MADS-box gene and which may therefore participate in the nutritional regulation of root architecture. BACKGROUND: The Arabidopsis ANR1 gene is a key regulator of root architecture (Zhang and Forde, 1998): When ANR1 expression is suppressed (by antisense or co-suppression) the resulting lines are no longer able to proliferate their lateral roots in response to localised supplies of NO3- (Zhang and Forde, 1998). ANR1 encodes a root-specific member of the MADS box family of transcription factors and is thought to be a component of a signalling pathway that an external NO3- signal to increase meristematic activity in the lateral root meristem (Zhang et al., 1999). Samples: 6 GSM157305: Gan_1-1_wildtype-nitrate-minus(WNM)_Rep1_ATH1 GSM157306: Gan_1-3_wildtype-nitrate-minus(WNM)_Rep2_ATH1 GSM157307: Gan_1-2_mutant-nitrate-minus(ANM)_Rep1_ATH1 GSM157308: Gan_1-4_mutant-nitrate-minus(ANM)_Rep2_ATH1 GSM157309: Gan_1-5_wildtype-nitrate-continuous(WNC)_Rep1_ATH1 GSM157310: Gan_1-6_mutant-nitrate-continuous(ANC)_Rep1_ATH1 39: GSE6823 record: The molecular basis of plant insect interactions [Arabidopsis thaliana] Summary: The aim of this study is to identify Arabidopsis genes whose expression is altered by aphid feeding. An understanding of the plant aphid interaction at the level of the plant transcriptome will 1) consolidate current areas of investigation focused on the phloem composition (the aphid diet), 2) open up areas of plant aphid interactions for ourselves and other workers, 3) Contribute to understanding the use of new molecular technologies in an environmental context and 4) contribute to existing and development of novel control strategies.Our Arabidopsis/Myzus persicae system provides a valuable model for the study because of: a) the advantages of using Arabidopsis, b) The ability to use clonal insects, c) phloem feeding aphids facilitate focus on a specific cell type, d) aphid stylectomy allows collection of pure phloem sap to monitor phloem phenotype of the plant and the insect diet, e) we have techniques to monitor the reproductive performance and feeding behaviour aphids.Our strategy has been to test the function of selected genes, particularly those regulating phloem composition (the feeding site of the aphid) based on current phloem models of phloem function. Samples: 6 GSM157299: JPritchard_A-1_CTR_Rep1_ATH1 GSM157300: JPritchard_A-2_CTR_Rep2_ATH1 GSM157301: JPritchard_A-3_CTR_Rep3_ATH1 GSM157302: JPritchard_A-4_API_Rep1_ATH1 GSM157303: JPritchard_A-5_API_Rep2_ATH1 GSM157304: JPritchard_A-6_API_Rep3_ATH1 40: GSE6158 record: Investigating the between organic acid and carbohydrate regulation of gene expression. [Arabidopsis thaliana] Summary: Arabidopsis acetate non-utilizing mutants were isolated based on fluoroacetate resistant germination. Interestingly, a number of these mutants exhibited altered developmental characteristics in response to exogenous sucrose supply, such as bleaching of the cotyledons. A preliminary microarray experiment has already been conducted on one of the mutants, acn1-2. The gene expression analysis was done using 3 day-old seedlings of acn1-2 and the parent, Col-7, which were germinated on agar plates with and without exogenous sucrose. A cross-comparison of acn1-2 and Col-7 revealed that the expression of a number of carbohydrate responsive genes was altered in the mutant. The request for further microarray analysis is to confirm this result. Samples: 12 GSM142687: MH001_ATH1_A1-grevi-CC1 GSM142688: MH001_ATH1_A2-grevi-CC2 GSM142689: MH001_ATH1_A3-grevi-CC3 GSM142690: MH001_ATH1_A4-grevi-AC1 GSM142691: MH001_ATH1_A5-grevi-AC2 GSM142692: MH001_ATH1_A6-grevi-AC3 GSM142693: MH001_ATH1_A7-grevi-CT1 GSM142694: MH001_ATH1_A8-grevi-CT2 GSM142695: MH001_ATH1_A9-grevi-CT3 GSM142696: MH001_ATH1_A10-grevi-AT1 GSM142697: MH001_ATH1_A11-grevi-AT2 GSM142698: MH001_ATH1_A12-grevi-AT3 41: GSE6155 record: Nutritional control of plant development: molecular analysis of the NO3- response pathway in Arabidopsis roots. [Arabidopsis thaliana] Summary: Background: The Arabidopsis ANR1 gene is a key regulator of root architecture (Zhang and Forde, 1998): when ANR1 is down-regulated (by antisense or co-suppression) the resulting lines are no longer able to proliferate their lateral roots in response to localised supplies of NO3- (Zhang and Forde, 1998). ANR1 encodes a root-specific member of the MADS box family of transcription factors and is thought to be a component of a signalling pathway that an external NO3- signal to increased meristematic activity in the lateral root meristem (Zhang et al., 1999).A major goal of our present BBSRC-funded project is to learn out this NO3- response pathway by identifying the downstream targets of ANR1. To this end we have generated a set of transgenic lines in which ANR1 is under a novel post-translational control. Samples: 7 GSM142669: SF002_ATH1_A7-Fille-ANGR4-12nodex GSM142670: SF002_ATH1_A8-Fille-ANGR4-12+dex GSM142671: SF001_ATH1_A1-Fille-WT-nodex GSM142672: SF001_ATH1_A2-Fille-WT-+dex GSM142673: SF001_ATH1_A3-Fille-ANGR4-12 GSM142674: SF002_ATH1_A5-Fille-WTnodex GSM142675: SF002_ATH1_A6-Fille-WT+dex 42: GSE6175 record: Clarification of the genetic basis of the iae1 and iae2 phenotypes [Arabidopsis thaliana] Summary: The mutants iae1 and iae2 have been mapped to two distinct loci on chromosome 2. With the aid of the GetCID service, we believe iae1 has been localised to a relatively small region (~100kb); while mapping has restricted iae2 to a small interval (~50kb) with a very limited number of candidate genes. Although it has proved difficult to determine which gene is mutated in iae1, we belive that use of the transcriptomics service will help identify which genes are affected (directly and indirectly) in this background. The iae2 locus is sufficiently restricted by genetics and by molecular data that identifying a candidate (and any downstream loci affected) should be straightforward. We require the use of the full genome chips. The data from this experiment should help tie together the data we ha. Samples: 9 GSM142820: PJ002_ATH1_A1-jarvis-iae1 GSM142821: PJ002_ATH1_A2-jarvis-iae1 GSM142822: PJ002_ATH1_A3-jarvis-iae1 GSM142823: PJ002_ATH1_A4-jarvis-iae2 GSM142824: PJ002_ATH1_A5-jarvis-iae2 GSM142825: PJ002_ATH1_A6-jarvis-iae2 GSM142826: PJ002_ATH1_A7-jarvis-B1798 GSM142827: PJ002_ATH1_A8-jarvis-B1798 GSM142828: PJ002_ATH1_A9-jarvis-B1798 43: GSE6174 record: Gene expression and carbohydrate metabolism through the diurnal cycle [Arabidopsis thaliana] Summary: This proposal is aimed at providing transcriptome data to underpin a long-term joint research programme of Steve Smith and Alison Smith. We are jointly studying starch synthesis and breakdown in Arabidopsis leaves, and individually studying other enzymes of carbohydrate metabolism (eg. sucrose synthases, invertases, sugar transporters). Collectively these enzymes are encoded by up to 100 known genes, but there are many others of relevance to our studies. For several years we have employed a defined set of growth conditions for this work (resulting in numerous publications). We have extensive data for changes in the amounts of starch, malto-oligosaccharides and sugars throughout the diurnal cycle in these plants, and we intend to quantitate numerous key enzymes. We now wish to profile changes in transcripts in these plants, so that this information can be correlated with changes in the amounts of key enzymes and metabolites. Samples: 22 GSM142798: SS001_ATH1_A1-Smith-21A GSM142799: SS001_ATH1_A2-Smith-22 GSM142800: SS001_ATH1_A3-Smith-23 GSM142801: SS001_ATH1_A4-Smith-1 GSM142802: SS001_ATH1_A5-Smith-5 GSM142803: SS001_ATH1_A6-Smith-8-45 GSM142804: SS001_ATH1_A7-Smith-10 GSM142805: SS001_ATH1_A8-Smith-11 GSM142806: SS001_ATH1_A9-Smith-13 GSM142807: SS001_ATH1_A10-Smith-17 GSM142808: SS001_ATH1_A11-Smith-21B GSM142809: SS002_ATH1_A1-smith-00h GSM142810: SS002_ATH1_A2-smith-01h GSM142811: SS002_ATH1_A3-smith-02h GSM142812: SS002_ATH1_A4-smith-04h GSM142813: SS002_ATH1_A5-smith-08h GSM142814: SS002_ATH1_A6-smith-12h GSM142815: SS002_ATH1_A7-smith-13h GSM142816: SS002_ATH1_A8-smith-14h GSM142817: SS002_ATH1_A9-smith-16h GSM142818: SS002_ATH1_A10-smith-20h GSM142819: SS002_ATH1_A11-smith-24h_repeat 44: GSE6172 record: The molecular basis of plant insect interactions. [Arabidopsis thaliana] Summary: The aim of this study is to identify Arabidopsis genes whose expression is altered by aphid feeding. An understanding of the plant aphid interaction at the level of the plant transcriptome will 1) consolidate current areas of investigation focused on the phloem composition (the aphid diet), 2) open up areas of plant aphid interactions for ourselves and other workers, 3) Contribute to understanding the use of new molecular technologies in an environmental context and 4) contribute to existing and development of novel control strategies.Our Arabidopsis/Myzus persicae system provides a valuable model for the study because of: a) the advantages of using Arabidopsis, b) The ability to use clonal insects, c) phloem feeding aphids facilitate focus on a specific cell type, d) aphid stylectomy allows collection of pure phloem sap to monitor ?phloem phenotype? of the plant and the insect diet, e) we have techniques to monitor the reproductive performance and feeding behaviour aphids.Our strategy has been to test the function of selected genes, particularly those regulating phloem composition (the feeding site of the aphid) based on current phloem models of phloem function. Samples: 6 GSM142788: JP001_ATH1_A1-Pritc-CTR GSM142789: JP001_ATH1_A2-Pritc-CTR GSM142790: JP001_ATH1_A3-Pritc-CTR_repeat GSM142791: JP001_ATH1_A4-Pritc-API GSM142792: JP001_ATH1_A5-Pritc-API GSM142793: JP001_ATH1_A6-Pritc-API 45: GSE5712 record: Transcriptome analysis of ARRESTED DEVELOPMENT 3 mutant. [Arabidopsis thaliana] Summary: Aims: Comparison of transcriptome between mutant and wild-type plant. Based on the temperature sensitive period of the mutant the gene likely acts during the earliest stages of the specification of the leaf primordium. Background: The ARRESTED DEVELOPMENT 3 mutation causes a temperature dependent loss of all spongy mesophyll and most palisade parenchyma in developing leaves. Although these leaves lack most internal tissues excepting vasculature they continue to expand away from the main axis of plant growth. Mature leaves have a small midrib and marginal regions that are large balloons of epidermis covering airspace. add3 is a temperature sensitive mutation whose most severe phenotypic response occurs at a restrictive temperature of 29 degrees C. Using BAC and TAC filters a recombinant population we have generated and available and newly developed molecular markers a high resolution (1000 chromosomes scored) physical genetic map has been completed to define the physical extent of the locus. Samples: 4 GSM133409: Pickett_1-3_wild-type_Rep1_ATH1 GSM133410: Pickett_1-1_ADD3_Rep1_ATH1 GSM133411: Pickett_1-4_wild-type_Rep2_ATH1 GSM133412: Pickett_1-2_ADD3_Rep2_ATH1 46: GSE6166 record: Genes affected by hog1 alleviation of CHS silencing [Arabidopsis thaliana] Summary: As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Samples: 8 GSM142756: NJ001_ATH1_A1-Jor-ECG-1.1 GSM142757: NJ001_ATH1_A2-Jor-ECG-1.2 GSM142758: NJ001_ATH1_A3-Jor-ECG-1.3 GSM142759: NJ001_ATH1_A4-Jor-ECG-1.4 GSM142760: NJ001_ATH1_A5-Jor-15B-2.1 GSM142761: NJ001_ATH1_A6-Jor-15B-2.2 GSM142762: NJ001_ATH1_A7-Jor-15B-2.3 GSM142763: NJ001_ATH1_A8-Jor-15B-2.4 47: GSE6165 record: The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue. [Arabidopsis thaliana] Summary: Aim: To determine the effect of an AtrbohC mutation on the gene expression pattern in primary root tissue, to identify candidate genes acting downstream of AtrbohC, particularly any encoding antioxidant-related proteins, signal transduction components or proteins known to be required for normal root-hair development. Background: Root-hairs are a model system for investigating plant cell polarity. The root-hair mutant rhd2 (Schiefelbein and Somerville, 1990. Plant Cell, 2:235) has short hairs that burst at their tips, (Jones and Smirnoff, unpublished). RHD2 has been cloned and is identical to AtrbohC (L. Dolan, pers. comm.), which encodes a homologue of the superoxide-generating neutrophil respiratory burst oxidase catalytic subunit gp91phox (Torres et al., 1998. Plant J., 14:365). Superoxide rapidly dismutates to hydrogen peroxide (H2O2), suggesting that the rhd2 phenotype may result from reduced H2O2 levels in root-hair cells. Samples: 6 GSM142750: MJ001_ATH1_A1-jones-WT1 GSM142751: MJ001_ATH1_A2-jones-WT2 GSM142752: MJ001_ATH1_A3-jones-rh1 GSM142753: MJ001_ATH1_A4-jones-rh2 GSM142754: MJ001_ATH1_A5-jones-WT-Rep3 GSM142755: MJ001_ATH1_A6-jones-RH-Rep3 48: GSE5749 record: A gene expression map of the Arabidopsis root [Arabidopsis thaliana] Summary: This experiment was donated by Philip N. Benfey's lab through ArexDB (http://www.arexdb.org). A global map of gene expression within an organ can identify genes with coordinated expression in localized domains, thereby relating gene activity to cell fate and tissue specialization. Here, we present localization of expression of an 22,000 genes in the Arabidopsis root. Gene expression was mapped to 15 different zones of the root that correspond to cell types and tissues at progressive developmental stages. Patterns of gene expression traverse traditional anatomical boundaries and show cassettes of hormonal response. Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics. Ex. Samples: 27 GSM133968: Birnbaum_1-19_LRC-1_Rep1_ATH1 GSM133969: Birnbaum_1-20_LRC-2_Rep2_ATH1 GSM133970: Birnbaum_1-21_LRC-3_Rep3_ATH1 GSM133971: Birnbaum_1-1_src5-1_Rep1_ATH1 GSM133972: Birnbaum_1-2_src5-2_Rep2_ATH1 GSM133973: Birnbaum_1-3_src5-3_Rep3_ATH1 GSM133974: Birnbaum_1-4_StageI-1_Rep1_ATH1 GSM133975: Birnbaum_1-5_StageI-2_Rep2_ATH1 GSM133976: Birnbaum_1-6_StageI-3_Rep3_ATH1 GSM133977: Birnbaum_1-7_StageI-4_Rep4_ATH1 GSM133978: Birnbaum_1-8_StageII-1_Rep1_ATH1 GSM133979: Birnbaum_1-9_StageII-2_Rep2_ATH1 GSM133980: Birnbaum_1-10_StageII-3_Rep3_ATH1 GSM133981: Birnbaum_1-11_StageII-4_Rep4_ATH1 GSM133982: Birnbaum_1-12_StageIII-1_Rep1_ATH1 GSM133983: Birnbaum_1-13_StageIII-2_Rep2_ATH1 GSM133984: Birnbaum_1-14_StageIII-3_Rep3_ATH1 GSM133985: Birnbaum_1-15_StageIII-4_Rep4_ATH1 GSM133986: Birnbaum_1-16_wol-1_Rep1_ATH1 GSM133987: Birnbaum_1-17_wol-2_Rep2_ATH1 GSM133988: Birnbaum_1-18_wol-3_Rep3_ATH1 GSM133989: Birnbaum_1-22_gl2-1_Rep1_ATH1 GSM133990: Birnbaum_1-23_gl2-2_Rep2_ATH1 GSM133991: Birnbaum_1-24_gl2-3_Rep3_ATH1 GSM133992: Birnbaum_1-25_J0571-1_Rep1_ATH1 GSM133993: Birnbaum_1-26_J0571-2_Rep2_ATH1 GSM133994: Birnbaum_1-27_J0571-3_Rep3_ATH1 49: GSE6832 record: Cytokinin treatment on aerial parts of seedlings [Arabidopsis thaliana] Summary: In Arabidopsis thaliana, the immediate early response of plants to cytokinin is formulated as the multistep AHK-AHP-ARR phosphorelay signaling circuitry, which is initiated by the cytokinin-receptor histidine protein kinases. In the hope of finding components (or genes) that function downstream of the cytokinin-mediated His-Asp phosphorelay signaling circuitry, we carried out genome-wide microarray analyses. To this end, we focused on a pair of highly homologous ARR10 and ARR12 genes by constructing an arr10 arr12 double null mutant. The mutant alleles used in this study were arr10-5 and arr12-1. arr10-5 is the SALK_098604 T-DNA insertion line, whose mutation was determined to be located in the fifth exon of the ARR10 coding sequence. Arr12-1 is the SALK_054752 T-DNA insertion line, whose mutation was determined to be located in the third exon of the ARR12 coding sequence. Samples: 12 GSM157382: Sakakibara_1-1_TZ-treatment-wild_Rep1_ATH1 GSM157383: Sakakibara_1-2_TZ-treatment-wild_Rep2_ATH1 GSM157384: Sakakibara_1-3_TZ-treatment-wild_Rep3_ATH1 GSM157385: Sakakibara_1-4_TZ-treatment-mutant_Rep1_ATH1 GSM157386: Sakakibara_1-5_TZ-treatment-mutant_Rep2_ATH1 GSM157387: Sakakibara_1-6_TZ-treatment-mutant_Rep3_ATH1 GSM157388: Sakakibara_1-7_DMSO-treatment-wild_Rep1_ATH1 GSM157389: Sakakibara_1-8_DMSO-treatment-wild_Rep2_ATH1 GSM157390: Sakakibara_1-9_DMSO-treatment-wild_Rep3_ATH1 GSM157391: Sakakibara_1-10_DMSO-treatment-mutant_Rep1_ATH1 GSM157392: Sakakibara_1-11_DMSO-treatment-mutant_Rep2_ATH1 GSM157393: Sakakibara_1-12_DMSO-treatment-mutant_Rep3_ATH1 50: GSE6150 record: Gibberellin and ethylene cross-talk at the level of transcriptional regulation in Arabidopsis. [Arabidopsis thaliana] Summary: This work is part of an existing collaboration between the two laboratories, funded by the EU (EU-RTN-INTEGA). Both parties will share the cost of this microarray experiment. Background: We have demonstrated that ethylene-insensitive mutants and wild type(col-0) Arabidopsis plants treated with an ethylene perception inhibitor have increased levels of expression of genes, such as GASA1 and g-TIP, that are thought to be regulated by GA (Vriezen et al, unpublished results). However, this observation was based on an RNA gel blot analysis and therefore limited to few genes. Aim: To investigate whether plants with decreased ethylene perception are generally hypersensitive to GA or whether this effect is restricted to specific genes. We plan to undertake a complete transcriptome analysis of GA-treated wild type andetr1-1 plants. Samples: 18 GSM142605: DV001_ATH1_A10-degra-Eg3_repeat2 GSM142606: DV001_ATH1_A1-degra-Cc0_repeat GSM142607: DV001_ATH1_A2-degra-Cc1_repeat2 GSM142608: DV001_ATH1_A3-degra-Cgh_repeat2 GSM142609: DV001_ATH1_A4-degra-Cg1_repeat2 GSM142610: DV001_ATH1_A5-degra-Cg3 GSM142611: DV001_ATH1_A6-degra-Ec0_repeat2 GSM142612: DV001_ATH1_A7-degra-Ec1 GSM142613: DV001_ATH1_A8-degra-Egh GSM142614: DV001_ATH1_A9-degra-Eg1_repeat2 GSM142615: DV002_ATH1_A2-degra-Cc1a GSM142616: DV002_ATH1_A2-degra-Cc1b GSM142617: DV002_ATH1_A4-degra-Cg1a GSM142618: DV002_ATH1_A4-degra-Cg1b GSM142619: DV002_ATH1_A7-degra-Ec1a GSM142620: DV002_ATH1_A7-degra-Ec1b GSM142621: DV002_ATH1_A9-degra-Eg1a GSM142622: DV002_ATH1_A9-degra-Eg1b 51: GSE6149 record: Targets of the mci genes. [Arabidopsis thaliana] Summary: In Antirrhinum, the equivalent mutant to the Arabidopsis cuc1 cuc2 double is called cup. We have cloned CUP and shown that it encodes a NAC-domain transcription factor homologous to CUC1 and CUC2. Yeast two-hybrid analysis shows that CUP interacts with TIC, an Antirrhinum TCP transcription factor. Moving back to Arabidopsis, the closest homologues to TIC encode TCP factors TCP13 and TCP14 which, we have now shown, also interact in two-hybrid experiments with CUC1 and CUC2. We have identified insertions in both TCP13 and TCP14. CUP, CUC1 and CUC2 play a role in the establishment of boundaries between lateral organs. As evolutionarily conserved interactors, we expect TCP13 and TCP14 to act in the same process. Homozygous tcp13 mutant flowers show mixed cell identity (mci) with the boundaries of organ identity out of register with those of physical organ development. Samples: 8 GSM142597: BD001_ATH1_A1-DAVIE-CON GSM142598: BD001_ATH1_A2-DAVIE-CON GSM142599: BD001_ATH1_A3-DAVIE-T13 GSM142600: BD001_ATH1_A4-DAVIE-T13 GSM142601: BD001_ATH1_A5-DAVIE-T14 GSM142602: BD001_ATH1_A6-DAVIE-T14 GSM142603: BD001_ATH1_A7-DAVIE-HET GSM142604: BD001_ATH1_A8-Davie-HET_repeat 52: GSE6148 record: The trans-differentiation of cultured Arabidopsis cells [Arabidopsis thaliana] Summary: The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Samples: 6 GSM142591: DB001_ATH1_A1-Brown-cal GSM142592: DB001_ATH1_A2-Brown-cal GSM142593: DB001_ATH1_A3-Brown-cal GSM142594: DB001_ATH1_A4-Brown-cal GSM142595: DB001_ATH1_A5-Brown-cal GSM142596: DB001_ATH1_A6-Brown-cal 53: GSE5701 record: AtGenExpress: Basic hormone treatment of seeds [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 12 GSM133311: RIKEN-LI1A GSM133312: RIKEN-LI1B GSM133313: RIKEN-LI2A GSM133314: RIKEN-LI2B GSM133315: RIKEN-LI3A GSM133316: RIKEN-LI3B GSM133317: RIKEN-LI4A GSM133318: RIKEN-LI4B GSM133319: RIKEN-LI5A GSM133320: RIKEN-LI5B GSM133321: RIKEN-LI6A GSM133322: RIKEN-LI6B 54: GSE5699 record: AtGenExpress: ARR21C overexpression [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 6 GSM133297: NO.13 GSM133298: NO.14 GSM133299: NO.15 GSM133300: NO.25 GSM133301: NO.26 GSM133302: NO.27 55: GSE5633 record: AtGenExpress: Developmental series (shoots and stems) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 42 GSM131643: ATGE_2_A GSM131644: ATGE_2_B GSM131645: ATGE_2_C GSM131646: ATGE_4_A GSM131647: ATGE_4_B GSM131648: ATGE_4_C GSM131649: ATGE_6_A GSM131650: ATGE_6_B GSM131651: ATGE_6_C GSM131652: ATGE_8_A GSM131653: ATGE_8_B GSM131654: ATGE_8_C GSM131655: ATGE_27_A GSM131656: ATGE_27_B GSM131657: ATGE_27_C GSM131658: ATGE_28_A2 GSM131659: ATGE_28_B2 GSM131660: ATGE_28_C2 GSM131661: ATGE_29_A2 GSM131662: ATGE_29_B2 GSM131663: ATGE_29_C2 GSM131664: ATGE_46_A GSM131665: ATGE_46_B GSM131666: ATGE_46_C GSM131667: ATGE_47_A GSM131668: ATGE_47_B GSM131669: ATGE_47_C GSM131670: ATGE_48_A GSM131671: ATGE_48_B GSM131672: ATGE_48_C GSM131673: ATGE_49_A GSM131674: ATGE_49_B GSM131675: ATGE_49_C GSM131676: ATGE_50_A GSM131677: ATGE_50_B GSM131678: ATGE_50_C GSM131679: ATGE_51_A GSM131680: ATGE_51_B GSM131681: ATGE_51_C GSM131682: ATGE_52_A GSM131683: ATGE_52_B GSM131684: ATGE_52_C 56: GSE5626 record: AtGenExpress: Stress Treatments (UV-B stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 28 GSM131383: AtGen_6-7711_UV-Bstress-Shoots-0.25h_Rep1 GSM131384: AtGen_6-7712_UV-Bstress-Shoots-0.25h_Rep2 GSM131385: AtGen_6-7721_UV-Bstress-Roots-0.25h_Rep1 GSM131386: AtGen_6-7722_UV-Bstress-Roots-0.25h_Rep2 GSM131387: AtGen_6-7111_UV-Bstress-Shoots-0.5h_Rep1 GSM131388: AtGen_6-7112_UV-Bstress-Shoots-0.5h_Rep2 GSM131389: AtGen_6-7121_UV-Bstress-Roots-0.5h_Rep1 GSM131390: AtGen_6-7122_UV-Bstress-Roots-0.5h_Rep2 GSM131391: AtGen_6-7211_UV-Bstress-Shoots-1.0h_Rep1 GSM131392: AtGen_6-7212_UV-Bstress-Shoots-1.0h_Rep2 GSM131393: AtGen_6-7221_UV-Bstress-Roots-1.0h_Rep1 GSM131394: AtGen_6-7222_UV-Bstress-Roots-1.0h_Rep2 GSM131395: AtGen_6-7311_UV-Bstress-Shoots-3.0h_Rep1 GSM131396: AtGen_6-7312_UV-Bstress-Shoots-3.0h_Rep2 GSM131397: AtGen_6-7321_UV-Bstress-Roots-3.0h_Rep1 GSM131398: AtGen_6-7322_UV-Bstress-Roots-3.0h_Rep2 GSM131399: AtGen_6-7411_UV-Bstress-Shoots-6.0h_Rep1 GSM131400: AtGen_6-7412_UV-Bstress-Shoots-6.0h_Rep2 GSM131401: AtGen_6-7421_UV-Bstress-Roots-6.0h_Rep1 GSM131402: AtGen_6-7422_UV-Bstress-Roots-6.0h_Rep2 GSM131403: AtGen_6-7511_UV-Bstress-Shoots-12.0h_Rep1 GSM131404: AtGen_6-7512_UV-Bstress-Shoots-12.0h_Rep2 GSM131405: AtGen_6-7521_UV-Bstress-Roots-12.0h_Rep1 GSM131406: AtGen_6-7522_UV-Bstress-Roots-12.0h_Rep2 GSM131407: AtGen_6-7611_UV-Bstress-Shoots-24.0h_Rep1 GSM131408: AtGen_6-7612_UV-Bstress-Shoots-24.0h_Rep2 GSM131409: AtGen_6-7621_UV-Bstress-Roots-24.0h_Rep1 GSM131410: AtGen_6-7622_UV-Bstress-Roots-24.0h_Rep2 57: GSE5624 record: AtGenExpress: Stress Treatments (Drought stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 28 GSM131331: AtGen_6-4711_Droughtstress-Shoots-0.25h_Rep1 GSM131332: AtGen_6-4712_Droughtstress-Shoots-0.25h_Rep2 GSM131333: AtGen_6-4721_Droughtstress-Roots-0.25h_Rep1 GSM131334: AtGen_6-4722_Droughtstress-Roots-0.25h_Rep2 GSM131335: AtGen_6-4111_Droughtstress-Shoots-0.5h_Rep1 GSM131336: AtGen_6-4112_Droughtstress-Shoots-0.5h_Rep2 GSM131337: AtGen_6-4121_Droughtstress-Roots-0.5h_Rep1 GSM131338: AtGen_6-4122_Droughtstress-Roots-0.5h_Rep2 GSM131339: AtGen_6-4211_Droughtstress-Shoots-1.0h_Rep1 GSM131340: AtGen_6-4212_Droughtstress-Shoots-1.0h_Rep2 GSM131341: AtGen_6-4221_Droughtstress-Roots-1.0h_Rep1 GSM131342: AtGen_6-4222_Droughtstress-Roots-1.0h_Rep2 GSM131343: AtGen_6-4311_Droughtstress-Shoots-3.0h_Rep1 GSM131344: AtGen_6-4312_Droughtstress-Shoots-3.0h_Rep2 GSM131345: AtGen_6-4321_Droughtstress-Roots-3.0h_Rep1 GSM131346: AtGen_6-4322_Droughtstress-Roots-3.0h_Rep2 GSM131347: AtGen_6-4411_Droughtstress-Shoots-6.0h_Rep1 GSM131348: AtGen_6-4412_Droughtstress-Shoots-6.0h_Rep2 GSM131349: AtGen_6-4421_Droughtstress-Roots-6.0h_Rep1 GSM131350: AtGen_6-4422_Droughtstress-Roots-6.0h_Rep2 GSM131351: AtGen_6-4511_Droughtstress-Shoots-12.0h_Rep1 GSM131352: AtGen_6-4512_Droughtstress-Shoots-12.0h_Rep2 GSM131353: AtGen_6-4521_Droughtstress-Roots-12.0h_Rep1 GSM131354: AtGen_6-4522_Droughtstress-Roots-12.0h_Rep2 GSM131355: AtGen_6-4611_Droughtstress-Shoots-24.0h_Rep1 GSM131356: AtGen_6-4612_Droughtstress-Shoots-24.0h_Rep2 GSM131357: AtGen_6-4621_Droughtstress-Roots-24.0h_Rep1 GSM131358: AtGen_6-4622_Droughtstress-Roots-24.0h_Rep2 58: GSE5619 record: Functional studies of a new Arabidopsis SH2 domain-containing gene [Arabidopsis thaliana] Summary: The protein modules known as SH2 (Src-homology-2) domains are key players in the signal transduction of animals. Two questions arise: Do such modules exist in plants, and when did SH2 domains evolve? Here I show that the Arabidopsis genome contains three strong candidates for plant SH2 proteins (referred to as PASTA1, 2 and 3 : GI:25513455, At1g78540, At1g17040 respectively) with homology to the SH2 domains and the adjacent linker region of STAT proteins (Signal Transducer and Activator of Transcription). The three characteristics features of a STAT protein sequence1, namely, (i) the SH2 domain with a conserved arginine residue crucial for binding to a phospho-tyrosine residue (ii) a tyrosine residue outside the C-terminus of the SH2-domain for phosphorylation during signalling and (iii) a DNA-binding domain, are conserved in the PASTA3 protein. Samples: 2 GSM131221: Kadalayil_1-1_wildtype_Rep1_ATH1 GSM131222: Kadalayil_1-2_Pasta2M1.1_Rep1_ATH1 59: GSE6160 record: Differential gene expression patterns in potassium-starved and caesium-treated plants [Arabidopsis thaliana] Summary: At high concentrations ceasium (Cs) is toxic to plant growth. This toxic effect may occur when Cs blocks potassium (K) uptake mechanisms in plants. Consequently, plants starved of K and plants exposed to toxic concentrations of Cs should have similar gene expression patterns. To test this hypothesis, Arabidopsis will initially be grown on agar containing 1/10 MS salts before being transferred to either 1/10 MS nutrient solution (control plants), 1/10 MS nutrient solution containing 2 mM Cs, or 1/10 MS nutrient solution with no K. Roots and shoot will then be harvested seven days after transfer and used to challenge ATH1 GeneChips. Samples: 18 GSM142703: JH003_ATH1_A1-Hammond-FS1 GSM142704: JH003_ATH1_A2-Hammond-KS1 GSM142705: JH003_ATH1_A3-Hammond-CS1 GSM142706: JH003_ATH1_A4-Hammond-FR1 GSM142707: JH003_ATH1_A5-Hammond-KR1_repeat GSM142708: JH003_ATH1_A6-Hammond-CR1 GSM142709: JH003_ATH1_A7-Hammond-FS2 GSM142710: JH003_ATH1_A8-Hammond-KS2 GSM142711: JH003_ATH1_A9-Hammond-CS2 GSM142712: JH003_ATH1_A10-Hammond-FR2 GSM142713: JH003_ATH1_A11-Hammond-KR2 GSM142714: JH003_ATH1_A12-Hommond-CR2_repeat GSM142715: JH003_ATH1_A13-Hammond-FS3 GSM142716: JH003_ATH1_A14-Hammond-KS3 GSM142717: JH003_ATH1_A15-Hammond-CS3 GSM142718: JH003_ATH1_A16-Hammond-FR3 GSM142719: JH003_ATH1_A17-Hammond-KR3 GSM142720: JH003_ATH1_A18-Hammond-CR3 60: GSE5744 record: Response to potassium starvation in roots [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org). This experiment studies the response of gene expression in roots of 25-35 day old plants grown on hydroponics after 6, 48 and 96 hours of potassium starvation. RNA from roots was extracted after transfer to control (control) or potassium free nutrient solution respectively (starvation). Experimenter name = Julian Schroeder Experimenter phone = 619-534-7759 Experimenter fax = 619-534-7108 Experimenter department = J Schroeder Laboratory Experimenter institute = University of California-San Diego Experimenter address = Biology Department Experimenter address = University of California-San Diego Experimenter address = La Jolla Experimenter zip/postal_code = CA 92093-0116 Experimenter country = USA Samples: 4 GSM133891: Schroeder_1-3_JS45-control-48h_Rep1_ATH1 GSM133892: Schroeder_1-6_JS43-control-96h_Rep1_ATH1 GSM133893: Schroeder_1-9_JS46-starve-48h_Rep1_ATH1 GSM133894: Schroeder_1-12_JS44-starve-96h_Rep1_ATH1 61: GSE5742 record: Response to ZAT12 expression [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor ZAT12. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Samples: 4 GSM133882: Zarka_4-1_MT-WTA(ZAT12)_Rep1_ATH1 GSM133883: Zarka_4-2_MT-WTB(ZAT12)_Rep2_ATH1 GSM133884: Zarka_4-3_MT-P15-15A_Rep1_ATH1 GSM133885: Zarka_4-4_MT-P15-8B_Rep2_ATH1 62: GSE5728 record: Environmental Genomics of calcicole-calcifuge physiology [Arabidopsis thaliana] Summary: Aim To identify genes which are differentially expressed between calcicoles and non- calcicoles. Background Grasslands on the calcareous soils of chalk and other limestones are among the most species-rich plant communities in Europe (Rodwell 1991 et seq.). They have experienced huge losses and remain vulnerable to such impacts as neglect of traditional management, agricultural improvement and global changes in climate, nitrogen depositions and ozone levels. Our understanding of the physiological characteristics of calcicoles and calcifuges remains limited. A detailed understanding of the genetic basis of the mechanisms that enable calcicoles to thrive on calcareous soils is essential to enable us to predict how these plant communities and their constituent species will be affected by environmental change and how the biodiversity of these ecosystems can be sustained.At Lancaster we have been studying calcicole-calcifuge physiology, with particular reference to Ca2+-tolerance, for over fifteen years. Samples: 8 GSM133739: Shirras_1-1_Calcicole_Rep1_ATH1 GSM133740: Shirras_1-2_Calcicole_Rep2_ATH1 GSM133741: Shirras_1-3_Non-Calcicole_Rep1_ATH1 GSM133742: Shirras_1-4_Non-Calcicole_Rep2_ATH1 GSM133743: Shirras_1-5_Calcicole_Rep3_ATH1 GSM133744: Shirras_1-6_Calcicole_Rep4_ATH1 GSM133745: Shirras_1-7_Non-Calcicole_Rep3_ATH1 GSM133746: Shirras_1-8_Non-Calcicole_Rep4_ATH1 63: GSE5726 record: Seedling transcriptome affected by Norflurazon-induced photobleaching of chloroplasts [Arabidopsis thaliana] Summary: Regulation of expression of genes encoding chloroplast components is critical to the autotrophic plant and never than in the cotyledons of the de-etiolating seedling. Many chloroplast proteins are nuclear-encoded and a retrograde signal from the chloroplasts (the Plastid Signal) modulates nuclear transcription. However, not all chloroplast-targeted genes are subject to this control and not all plastid-dependent nuclear genes are chloroplast-targeted. We therefore aim to provide the most comprehensive screen yet of which genes are affected by plastid-signalling. To specifically knock-out positive plastid signalling in light-grown cotyledons, the herbicide Norflurazon (NF) is supplied in the growth medium, causing a carotenoid deficiency that leaves the chloroplasts vulnerable to photobleaching. Samples: 6 GSM133723: McCormac_1-1_wildtype-NFtreated_Rep1_ATH1 GSM133724: McCormac_1-2_wildtype-Contrl_Rep1_ATH1 GSM133725: McCormac_1-3_mutant-NFtreated_Rep1_ATH1 GSM133726: McCormac_1-4_wildtype-NFtreated_Rep2_ATH1 GSM133727: McCormac_1-5_wildtype-Contrl_Rep2_ATH1 GSM133728: McCormac_1-6_mutant-NFtreated_Rep2_ATH1 64: GSE5710 record: Dark-induced gene expression in sfr6 [Arabidopsis thaliana] Summary: The sfr6 mutant was identified on the basis of its failure to cold acclimate, and exhibits a marked deficiency in cold-and osmotic stress-inducible gene expression (Knight et al., 1999). We have demonstrated that genes of this type (so-called COR genes) are misregulated if they contain the DRE (drought-responsive element, or CRT; C-repeat) cis acting element in their promoter (Boyce et al., 2003). Micro-array analysis has allowed us to identify a number of COR genes misregulated in sfr6, all of which contain the DRE element. However, these experiments have indicated that other genes, not of the COR group, are also misregulated in the mutant and these do not contain the DRE element. We chose the three non-COR genes that were most clearly down-regulated in sfr6 on our previous micro-array, and identified each as of these as dark-inducible. Samples: 4 GSM133399: Knight_2-1_wildtype-lt_Rep1_ATH1 GSM133400: Knight_2-3_sfr6-lt_Rep1_ATH1 GSM133401: Knight_2-2_wildtype-dk_Rep1_ATH1 GSM133402: Knight_2-4_sfr6-dk_Rep1_ATH1 65: GSE5735 record: Identification of Core Genes Regulating Plant Programmed Cell Death (PCD) [Arabidopsis thaliana] Summary: PCD is a highly organised process that is involved in development and in an organisms response to biotic stresses (toxins and avirulent pathogens) and abiotic stresses (such as temperature, water availability, etc.). It is a genetically regulated form of cellular suicide, however in plants the underlying process is poorly understood. Although PCD may occur in response to different stimuli; we believe once it is triggered, one core mechanism is responsible for the cellular demise. It is our aim to identify the elements of this mechanism. We will do this by expanding on the work of a previous user of GARNet's GeneChip microarray facility, Dr. Jodi Swidzinski. She utilised an Arabidopsis cell suspension system; performing microarray analysis on both senescing, and heat shock induced PCD samples. Samples: 8 GSM133808: Diamond_A-1-Diamo-fum_SLD GSM133809: Diamond_A-2-Diamo-fum_SLD GSM133810: Diamond_A-3-Diamo-fum_SLD GSM133811: Diamond_A-4-Diamo-fum_SLD GSM133812: Diamond_A-1-Diamo-met_SLD GSM133813: Diamond_A-2-Diamo-met_SLD GSM133814: Diamond_A-3-Diamo-met_SLD GSM133815: Diamond_A-4-Diamo-met_SLD 66: GSE5733 record: Characterisation of genetic basis of changes in stomatal numbers at elevated atmospheric carbon dioxide concentrations [Arabidopsis thaliana] Summary: Atmospheric CO2 concentrations can determine the number of stomata that form on plant leaves (Woodward & Kelly 1995 New Phyt 131: 311-327). The majority of species exhibit reduced stomatal densities at elevated CO2. However, not all plant species react in the same way to elevated CO2 levels and there is a spectrum of effects: Some species increase stomatal densities, some decrease stomatal densities, and some are unaffected. In addition to which, other environmental factors influence the number of stomata that a plant form. Light intensity has also been shown to affect stomatal numbers in various Arabidopsis ecotypes (Schluter et al. 2003 J Exp Bot 54 (383): 867-874; Lake et al. 2002 J Exp Bot 53 (367): 183-193), by increasing stomatal numbers with increasing light levels. There are many changes in gene expression under elevated CO2 conditions, so pinpointing specific genes involved in the stomatal response to CO2 is difficult. Samples: 6 GSM133794: Bird_1-1_high-light-ambientCO2_Rep1_ATH1 GSM133795: Bird_1-2_medium-light-ambientCO2_Rep1_ATH1 GSM133796: Bird_1-3_low-light-ambientCO2_Rep1_ATH1 GSM133797: Bird_1-4_high-light-highCO2_Rep1_ATH1 GSM133798: Bird_1-5_medium-light-highCO2_Rep1_ATH1 GSM133799: Bird_1-6_low-light-highCO2_Rep1_ATH1 67: GSE5685 record: AtGenExpress: Pathogen Series: Pseudomonas half leaf injection [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 32 GSM133037: 2508 GSM133038: 2783 GSM133039: 2510 GSM133040: 2784 GSM133041: 2525 GSM133042: 2527 GSM133043: 2785 GSM133044: 2786 GSM133045: 2787 GSM133046: 2788 GSM133047: 2789 GSM133048: 2790 GSM133049: 2792 GSM133050: 2791 GSM133051: 2793 GSM133052: 2795 GSM133053: 2794 GSM133054: 2796 GSM133055: 2797 GSM133056: 2798 GSM133057: 2504 GSM133058: 2506 GSM133059: 2507 GSM133060: 2509 GSM133061: 2511 GSM133062: 2512 GSM133063: 2526 GSM133064: 2528 GSM133065: 2529 GSM133066: 2503 GSM133067: 2505 GSM133068: 2530 68: GSE5758 record: Expression Level Polymorphism Project (ELP) - Mt-0 [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134448: St.Clair_1-73_291_Mt-0_0.02%-silwet_Rep1_ATH1 GSM134449: St.Clair_1-74_320_Mt-0_0.02%-silwet_Rep2_ATH1 GSM134450: St.Clair_1-75_376_Mt-0_0.02%-silwet_Rep3_ATH1 GSM134451: St.Clair_1-76_283_Mt-0_0.02%-silwet_Rep1_ATH1 GSM134452: St.Clair_1-77_302_Mt-0_0.02%-silwet_Rep2_ATH1 GSM134453: St.Clair_1-78_366_Mt-0_0.02%-silwet_Rep3_ATH1 GSM134454: St.Clair_1-79_276_Mt-0_0.02%-silwet_Rep1_ATH1 GSM134455: St.Clair_1-80_308_Mt-0_0.02%-silwet_Rep2_ATH1 GSM134456: St.Clair_1-81_356_Mt-0_0.02%-silwet_Rep3_ATH1 GSM134457: St.Clair_1-82_294_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134458: St.Clair_1-83_323_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134459: St.Clair_1-84_379_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134460: St.Clair_1-85_286b_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134461: St.Clair_1-86_305_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134462: St.Clair_1-87_370_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134463: St.Clair_1-88_280_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134464: St.Clair_1-89_314_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134465: St.Clair_1-90_360_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 69: GSE5753 record: Expression Level Polymorphism Project (ELP) - Cvi-1 [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134358: St.Clair_1-19_336_Cvi-1_0.02%-silwet_Rep1_ATH1 GSM134359: St.Clair_1-20_361_Cvi-1_0.02%-silwet_Rep2_ATH1 GSM134360: St.Clair_1-21_429_Cvi-1_0.02%-silwet_Rep3_ATH1 GSM134361: St.Clair_1-22_341_Cvi-1_0.02%-silwet_Rep1_ATH1 GSM134362: St.Clair_1-23_363_Cvi-1_0.02%-silwet_Rep2_ATH1 GSM134363: St.Clair_1-24_437_Cvi-1_0.02%-silwet_Rep3_ATH1 GSM134364: St.Clair_1-25_345_Cvi-1_0.02%-silwet_Rep1_ATH1 GSM134365: St.Clair_1-26_371_Cvi-1_0.02%-silwet_Rep2_ATH1 GSM134366: St.Clair_1-27_449_Cvi-1_0.02%-silwet_Rep3_ATH1 GSM134367: St.Clair_1-28_339_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134368: St.Clair_1-29_362_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134369: St.Clair_1-30_433_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134370: St.Clair_1-31_343_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134371: St.Clair_1-32_367_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134372: St.Clair_1-33_443_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134373: St.Clair_1-34_346_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134374: St.Clair_1-35_373_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134375: St.Clair_1-36_454b_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 70: GSE5751 record: The early post-germinative embryo and endosperm transcriptomes in Arabidopsis [Arabidopsis thaliana] Summary: Arabidopsis seed germination is coordinated with the strong induction of metabolic pathways required for the mobilisation and utilization of seed storage reserves. These are essential to support the seedling before the establishment of photoauxotrophic growth. The activity of genes encoding enzymes required for lipid mobilisation is regulated largely at the level of transcription, but our knowledge of how this regulation occurs is extremely limited. After germination the rate of lipid reserve mobilisation is determined by the carbohydrate status of the seedling and by the osmotic potential of the growth substrate. The plant response to both of these requires the action of the hormone abscisic acid (ABA). We have shown that this regulation is tissue specific (Penfield et al., 2004 Plant Cell 16, 2705-2718), and that although lipid breakdown in the embryo is inhibited by ABA, lipid breakdown in the endosperm tissues is not. Samples: 18 GSM134299: Penfield_1-1_endosperm-control_Rep1_ATH1 GSM134300: Penfield_1-2_endosperm-control_Rep2_ATH1 GSM134301: Penfield_1-3_endosperm-control_Rep3_ATH1 GSM134302: Penfield_1-4_endosperm-ABA_Rep1_ATH1 GSM134303: Penfield_1-5_endosperm-ABA_Rep2_ATH1 GSM134304: Penfield_1-6_endosperm-ABA_Rep3_ATH1 GSM134305: Penfield_1-7_endosperm-PAC_Rep1_ATH1 GSM134306: Penfield_1-8_endosperm-PAC_Rep2_ATH1 GSM134307: Penfield_1-9_endosperm-PAC_Rep3_ATH1 GSM134308: Penfield_1-10_embryo-control_Rep1_ATH1 GSM134309: Penfield_1-11_embryo-control_Rep2_ATH1 GSM134310: Penfield_1-12_embryo-control_Rep3_ATH1 GSM134311: Penfield_1-13_embryo-ABA_Rep1_ATH1 GSM134312: Penfield_1-14_embryo-ABA_Rep2_ATH1 GSM134313: Penfield_1-15_embryo-ABA_Rep3_ATH1 GSM134314: Penfield_1-16_embryo-PAC_Rep1_ATH1 GSM134315: Penfield_1-17_embryo-PAC_Rep2_ATH1 GSM134316: Penfield_1-18_embryo-PAC_Rep3_ATH1 71: GSE5700 record: AtGenExpress: Effect of ABA during seed imbibition [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 8 GSM133303: RIKEN-NAKABAYASHI1A GSM133304: RIKEN-NAKABAYASHI1B GSM133305: RIKEN-NAKABAYASHI2A GSM133306: RIKEN-NAKABAYASHI2B GSM133307: RIKEN-NAKABAYASHI3A GSM133308: RIKEN-NAKABAYASHI4A GSM133309: RIKEN-NAKABAYASHI4B GSM133310: RIKEN-NAKABAYASHI5B 72: GSE5616 record: AtGenExpress: Response to Phytophthora infestans [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC) The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 18 GSM131151: AtGen_C-1_1-C-6_REP1_ATH1 GSM131152: AtGen_C-2_2-C-6_REP2_ATH1 GSM131153: AtGen_C-3_4-C-6_REP3_ATH1 GSM131154: AtGen_C-4_1-C-12_REP1_ATH1 GSM131155: AtGen_C-5_2-C-12_REP2_ATH1 GSM131156: AtGen_C-6_3-C-12_REP3_ATH1 GSM131157: AtGen_C-7_1-C-24_REP1_ATH1 GSM131158: AtGen_C-8_2-C-24_REP2_ATH1 GSM131159: AtGen_C-9_3-C-24_REP3_ATH1 GSM131160: AtGen_C-10_1-Pi-6_REP1_ATH1 GSM131161: AtGen_C-11_2-Pi-6_REP2_ATH1 GSM131162: AtGen_C-12_3-Pi-6_REP3_ATH1 GSM131163: AtGen_C-13_1-Pi-12_REP1_ATH1 GSM131164: AtGen_C-14_2-Pi-12_REP2_ATH1 GSM131165: AtGen_C-15_3-Pi-12_REP3_ATH1 GSM131166: AtGen_C-16_1-Pi-24_REP1_ATH1 GSM131167: AtGen_C-17_2-Pi-24_REP2_ATH1 GSM131168: AtGen_C-18_3-Pi-24_REP3_ATH1 73: GSE5611 record: Differential gene expression patterns in the phosphate deficient mutant, pho 1 [Arabidopsis thaliana] Summary: Background: The UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yield and quality, since chemical assays of soil nutrients are unreliable. Excessive fertiliser applications are costly and can lead to unnecessary pollution. A possible solution is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression under incipient nutrient deficiency. Aim: The aim of this project is to use mutants with reduced leaf phosphate contents to identify genes upregulated in response to phosphate stress. Preliminary gene expression analysis has identified several phosphate responsive genes to be upregulated in the pho1 mutant. However, further replicates of the experiment are required to confirm these changes. Methods: Arabidopsis mutant pho1 (N8507) and its parent ecotype Columbia 2 (N907) will be grown on MS agar under identical conditions. Samples: 6 GSM131060: Hammond_2-1_Col2wildtype_Rep1_ATH1 GSM131061: Hammond_2-2_pho1mutant_Rep1_ATH1 GSM131062: Hammond_2-3_Col2wildtype_Rep2_ATH1 GSM131063: Hammond_2-4_pho1mutant_Rep2_ATH1 GSM131064: Hammond_2-5_Col2wildtype_Rep3_ATH1 GSM131065: Hammond_2-6_pho1mutant_Rep3_ATH1 74: GSE5641 record: Peroxisomal mdh mutant [Arabidopsis thaliana] Summary: The aim is to study the function of peroxisomal NAD-malate dehydrogenase in fatty acid beta-oxidation, glyoxylate cycle and photorespiration. Both peroxisomal MDH genes (At2g22780 and At5g09660) have been knocked out with T-DNA insertions and a double mutant made. Double mutant seedlings are blocked in beta-oxidation - they are 2,4DB resistant and beta-oxidation genes are repressed. They carry out glyoxylate cycle as normal. Plants grow well in soil and produce seed. Microarray analysis will tell us the extent of changes in gene expression in the mutant. For microarray analysis seeds are stratified at 4 C on agar medium with 1/2 strength M&S salts and 1% sucrose for 2 days, then seedlings grown for 2 days at 20 C in the light (100 umol/m2/s). Triplicate samples will be grown for mutant and wild type (col-0) and RNA isolated from each. Samples: 6 GSM131844: Pracharoenwattana_1-1_mdhA_Rep1_ATH1 GSM131845: Pracharoenwattana_1-2_mdhB_Rep2_ATH1 GSM131846: Pracharoenwattana_1-3_mdhC_Rep3_ATH1 GSM131847: Pracharoenwattana_1-4_ColA_Rep1_ATH1 GSM131848: Pracharoenwattana_1-5_ColB_Rep2_ATH1 GSM131849: Pracharoenwattana_1-6_ColC_Rep3_ATH1 75: GSE5636 record: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 1: Ambient CO2 and Ambient Light) [Arabidopsis thaliana] Summary: We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC. The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways. The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. Samples: 26 GSM131749: Quick_A2_1-2hr_Rep1_ATH1 GSM131750: Quick_A6_1-4hr-Rep1_ATH1 GSM131751: Quick_A10_1-12hr_Rep1_ATH1 GSM131752: Quick_A14_1-24hr_Rep1_ATH1 GSM131753: Quick_A18_1-48hr_Rep1_ATH1 GSM131754: Quick_A22_1-96hr_Rep1_ATH1 GSM131755: Quick_A28_1-2hr_Rep2_ATH1 GSM131756: Quick_A32_1-4hr-Rep2_ATH1 GSM131757: Quick_A36_1-12hr_Rep2_ATH1 GSM131758: Quick_A40_1-24hr_Rep2_ATH1 GSM131759: Quick_A44_1-48hr_Rep2_ATH1 GSM131760: Quick_A48_1-96hr_Rep2_ATH1 GSM131761: Quick_A54_1-2hr_Rep3_ATH1 GSM131762: Quick_A58_1-4hr-Rep3_ATH1 GSM131763: Quick_A62_1-12hr_Rep3_ATH1 GSM131764: Quick_A66_1-24hr_Rep3_ATH1 GSM131765: Quick_A70_1-48hr_Rep3_ATH1 GSM131766: Quick_A74_1-96hr_Rep3_ATH1 GSM131767: Quick_A80_1-2hr_Rep4_ATH1 GSM131768: Quick_A84_1-4hr-Rep4_ATH1 GSM131769: Quick_A88_1-12hr_Rep4_ATH1 GSM131770: Quick_A92_1-24hr_Rep4_ATH1 GSM131771: Quick_A96_1-48hr_Rep4_ATH1 GSM131772: Quick_A100_1-96hr_Rep4_ATH1 GSM131773: Quick_A105_1-24hr_Rep1m_ATH1 GSM131774: Quick_A109_1-24hr_Rep2m_ATH1 76: GSE5634 record: AtGenExpress: Developmental series (siliques and seeds) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 24 GSM131685: ATGE_76_A GSM131686: ATGE_76_B GSM131687: ATGE_76_C GSM131688: ATGE_77_D GSM131689: ATGE_77_E GSM131690: ATGE_77_F GSM131691: ATGE_78_D GSM131692: ATGE_78_E GSM131693: ATGE_78_F GSM131694: ATGE_79_A GSM131695: ATGE_79_B GSM131696: ATGE_79_C GSM131697: ATGE_81_A GSM131698: ATGE_81_B GSM131699: ATGE_81_C GSM131700: ATGE_82_A GSM131701: ATGE_82_B GSM131702: ATGE_82_C GSM131703: ATGE_83_A GSM131704: ATGE_83_B GSM131705: ATGE_83_C GSM131706: ATGE_84_A GSM131707: ATGE_84_B GSM131708: ATGE_84_D 77: GSE5627 record: AtGenExpress: Stress Treatments (Wounding stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 28 GSM131411: AtGen_6-8715_Woundingstress-Shoots-0.25h_Rep1 GSM131412: AtGen_6-8712_Woundingstress-Shoots-0.25h_Rep2 GSM131413: AtGen_6-8723_Woundingstress-Roots-0.25h_Rep1 GSM131414: AtGen_6-8724_Woundingstress-Roots-0.25h_Rep2 GSM131415: AtGen_6-8111_Woundingstress-Shoots-0.5h_Rep1 GSM131416: AtGen_6-8112_Woundingstress-Shoots-0.5h_Rep2 GSM131417: AtGen_6-8124_Woundingstress-Roots-0.5h_Rep1 GSM131418: AtGen_6-8126_Woundingstress-Roots-0.5h_Rep2 GSM131419: AtGen_6-8211_Woundingstress-Shoots-1.0h_Rep1 GSM131420: AtGen_6-8214_Woundingstress-Shoots-1.0h_Rep2 GSM131421: AtGen_6-8224_Woundingstress-Roots-1.0h_Rep1 GSM131422: AtGen_6-8225_Woundingstress-Roots-1.0h_Rep2 GSM131423: AtGen_6-8313_Woundingstress-Shoots-3.0h_Rep1 GSM131424: AtGen_6-8314_Woundingstress-Shoots-3.0h_Rep2 GSM131425: AtGen_6-8324_Woundingstress-Roots-3.0h_Rep1 GSM131426: AtGen_6-8325_Woundingstress-Roots-3.0h_Rep2 GSM131427: AtGen_6-8411_Woundingstress-Shoots-6.0h_Rep1 GSM131428: AtGen_6-8412_Woundingstress-Shoots-6.0h_Rep2 GSM131429: AtGen_6-8423_Woundingstress-Roots-6.0h_Rep1 GSM131430: AtGen_6-8424_Woundingstress-Roots-6.0h_Rep2 GSM131431: AtGen_6-8511_Woundingstress-Shoots-12.0h_Rep1 GSM131432: AtGen_6-8512_Woundingstress-Shoots-12.0h_Rep2 GSM131433: AtGen_6-8524_Woundingstress-Roots-12.0h_Rep1 GSM131434: AtGen_6-8525_Woundingstress-Roots-12.0h_Rep2 GSM131435: AtGen_6-8611_Woundingstress-Shoots-24.0h_Rep1 GSM131436: AtGen_6-8612_Woundingstress-Shoots-24.0h_Rep2 GSM131437: AtGen_6-8621_Woundingstress-Roots-24.0h_Rep1 GSM131438: AtGen_6-8622_Woundingstress-Roots-24.0h_Rep2 78: GSE5625 record: AtGenExpress: Stress Treatments (Genotoxic stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 24 GSM131359: AtGen_6-5111_Genotoxicstress-Shoots-0.5h_Rep1 GSM131360: AtGen_6-5112_Genotoxicstress-Shoots-0.5h_Rep2 GSM131361: AtGen_6-5121_Genotoxicstress-Roots-0.5h_Rep1 GSM131362: AtGen_6-5122_Genotoxicstress-Roots-0.5h_Rep2 GSM131363: AtGen_6-5211_Genotoxicstress-Shoots-1.0h_Rep1 GSM131364: AtGen_6-5212_Genotoxicstress-Shoots-1.0h_Rep2 GSM131365: AtGen_6-5221_Genotoxicstress-Roots-1.0h_Rep1 GSM131366: AtGen_6-5222_Genotoxicstress-Roots-1.0h_Rep2 GSM131367: AtGen_6-5311_Genotoxicstress-Shoots-3.0h_Rep1 GSM131368: AtGen_6-5312_Genotoxicstress-Shoots-3.0h_Rep2 GSM131369: AtGen_6-5321_Genotoxicstress-Roots-3.0h_Rep1 GSM131370: AtGen_6-5322_Genotoxicstress-Roots-3.0h_Rep2 GSM131371: AtGen_6-5411_Genotoxicstress-Shoots-6.0h_Rep1 GSM131372: AtGen_6-5412_Genotoxicstress-Shoots-6.0h_Rep2 GSM131373: AtGen_6-5421_Genotoxicstress-Roots-6.0h_Rep1 GSM131374: AtGen_6-5422_Genotoxicstress-Roots-6.0h_Rep2 GSM131375: AtGen_6-5511_Genotoxicstress-Shoots-12.0h_Rep1 GSM131376: AtGen_6-5512_Genotoxicstress-Shoots-12.0h_Rep2 GSM131377: AtGen_6-5521_Genotoxicstress-Roots-12.0h_Rep1 GSM131378: AtGen_6-5522_Genotoxicstress-Roots-12.0h_Rep2 GSM131379: AtGen_6-5611_Genotoxicstress-Shoots-24.0h_Rep1 GSM131380: AtGen_6-5612_Genotoxicstress-Shoots-24.0h_Rep2 GSM131381: AtGen_6-5621_Genotoxicstress-Roots-24.0h_Rep1 GSM131382: AtGen_6-5622_Genotoxicstress-Roots-24.0h_Rep2 79: GSE6168 record: Comparison of the transcript profile of the auxin resistant axr4 mutant and wild-type Col0 [Arabidopsis thaliana] Summary: The plant hormone auxin represents an important regulator of growth and development. Significant insight into the mechanisms of auxin action have been obtained from studies of auxin resistant mutants such as aux1 and axr3. The Arabidopsis axr4 mutant was identified in a screen for auxin resistant root growth. In addition to the root growth of axr4 being resistant to exogenous auxin, there is also a 50% reduction in the number of lateral roots that form. The double axr4/aux1 mutant shows an additive effect in reducing lateral root numbers to 10% of wild-type. Gaining further information about the potential interaction between AUX1 and AXR4 may provide important insight into auxin regulated plant growth. Mapping experiments have placed the AXR4 gene on the lower arm of chromosome 1 between the ch1 and le markers (Hobbie and Estelle 1995). Samples: 2 GSM142770: AM001_ATH1_axr4-2 GSM142771: AM001_ATH1_Control 80: GSE5743 record: Whole genome expression in response to herbicidal levels of 2,4-D application [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://www.arabidopsis.org). In this experiment we examined whole genome response to herbicidal levels of 2,4-D application. Arabidopsis plants (14 days) grown in vitro on MS medium in petri dishes were flooded with 1 mL stock of 2,4-D to enable root uptake. Plants were treated with 1.0 mM 2,4-D for a period of 1 hour immediately after which RNA was extracted and used for the microarray based experiments. the goal of this study was to explore the herbicidal mode of action of auxinic herbicide 2,4-D. Experimenter name = Chitra Raghavan Experimenter department = Trevor Stevenson Laboratory Experimenter institute = IRRI Experimenter address = Entomology and Plant Pathology Division IRRI Experimenter zip/postal_code = Manila 4031 Experimenter country = P. Samples: 3 GSM133887: Raghavan_1-1_CONTROL_Rep1_ATH1 GSM133888: Raghavan_1-2_1MM-1HR-A_Rep1_ATH1 GSM133889: Raghavan_1-3_1MM-1HR-B_Rep2_ATH1 81: GSE5727 record: The effects of mutants in stress response pathways on gene expression during senescence [Arabidopsis thaliana] Summary: Many signalling pathways are involved in controlling gene expression during plant senescence. Pathways involving SA, JA and ethylene have a role in senescence but none are essential for the senescence process to occur. The aim of this experiment is to classify senescence-enhanced genes into groups depending on the signalling pathways that regulate them. This will provide useful information on the relative importance of each signalling pathway during senescence and allow us to separate potential senescence-specific genes and pathways from the stress response pathways.Mutants in genes in the ethylene pathway (ein2) and the jasmonate pathway (coi1) and the NahG transgenic plant which is defective in the salicylic acid pathway will be grown until the mid flowering stage. Fully developed green and partially senescent leaves will be harvested from the plants at this stage. Samples: 10 GSM133729: Buchanan-Wollaston_A-1-bwoll-C0G_SLD GSM133730: Buchanan-Wollaston_A-2-bwoll-C5G_SLD GSM133731: Buchanan-Wollaston_A-3-bwoll-C0S_SLD GSM133732: Buchanan-Wollaston_A-4-bwoll-C5S_SLD GSM133733: Buchanan-Wollaston_A-5-bwoll-NG1_SLD GSM133734: Buchanan-Wollaston_A-6-bwoll-NG2_SLD GSM133735: Buchanan-Wollaston_A-7-bwoll-Ei1_SLD GSM133736: Buchanan-Wollaston_A-8-bwoll-Ei2_SLD GSM133737: Buchanan-Wollaston_A-9-bwoll-Co1_SLD GSM133738: Buchanan-Wollaston_A-10-bwoll-Co2_SLD 82: GSE5725 record: Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana [Arabidopsis thaliana] Summary: Agrobacterium tumefaciens, a bacterial species found in temperate soils world wide, is the causative agent of crown gall disease on many plants. A. tumefaciens-induced tumours are feared in orchards and vineyards because of their pathological interference with nutrient and water supply which results in crop decline. Small wounds at the crown of the plant, usually induced by wind-bending, are potential entry sites for the bacterium. The tumorous growth is initiated by the integration and expression of the T-DNA of the bacterial Ti plasmid within the plant nuclear DNA. The T-DNA encodes enzymes catalysing the synthesis of increased concentrations of auxin and cytokinin, and of opines which stimulate cell division and enlargement. The fast growing tumours have been shown to be a strong nutrient sink on their host plants. Samples: 4 GSM133719: Deeken_A-1-Deeke-Tum_SLD_REP1 GSM133720: Deeken_A-2-Deeke-Inf_SLD_REP1 GSM133721: Deeken_A-1-Deeke-Tum_SLD_REP2 GSM133722: Deeken_A-2-Deeke-Inf_SLD_REP2 83: GSE5711 record: Cold induced changes: differences between the Arabidopsis thaliana wild type and freezing sensitive mutants. [Arabidopsis thaliana] Summary: Arabidopsis sfr mutants are deficient in cold acclimation during exposure to coolnon-freezing temperatures. Although not visibly affected by the cold they have lost the ability to survive subsequent freezing. We plan to investigate how the sfr2 and sfr6 mutants respond to low temperature on the gene expression level. Wild type plants that have undergone identical treatments in parallel are necessary controls. The cold treatment of plants in the rosette stage (soil grown in a 8/16 hours day/night cycle) will be carried out in a cooled growth chamber at 4 degrees for 24 hours (same light regimetreatment starting/ending at the 4th hour of light). The aerial parts of the treated and untreated plants will be collected and frozen immediately in liquid nitrogen for RNA extraction. Comparison of the cold response of thousands of Arabidopsis genes in the wild type to the situation in our freezing sensitive mutants will enhance our understanding of the cold response itself and illuminate the effect of the mutations on the cold acclimation process. Samples: 6 GSM133403: Bramke_A3-warre-S6C GSM133404: Bramke_A4-warre-S6W GSM133405: Bramke_A5-warre-S2C GSM133406: Bramke_A6-warre-S2W GSM133407: Bramke_A1-warre-WTC GSM133408: Bramke_A2-warre-WTW 84: GSE5736 record: To identify changes in gene expression during silique senescence in Arabidopsis thaliana [Arabidopsis thaliana] Summary: The aim of the experiment is to compare and contrast the profiles of gene expression during silique senescence and to identify the molecular events that regulate the timing of the process. Silique occurs over a highly predictable time frame and as a consequence it may be easier to identify the molecular events that are critical for the process to take place than in systems such as leaf senescence. The material will be collected from 20 Arabidopsis thaliana ecotype Columbia plants (NASC order number N1093) grown under controlled conditions specified under NASC protocol: Baseline sample preparation. Two pods will be collected from each plant and pooled from 20 plants to reduce sampling variability. It is intended that 3 replicates of the experiment will be submitted. The RNA will be extracted from mature green silique tissues of 10 days after anthesis and senescing pod tissues of 20 days after anthesis using lithium chloride extraction protocol and cleaned with Qiagen RNAeasy column. Samples: 6 GSM133816: Yang_1-1_young-pod_Rep1_ATH1 GSM133817: Yang_1-2_old-pod_Rep1_ATH1 GSM133818: Yang_1-3_young-pod_Rep2_ATH1 GSM133819: Yang_1-4_old-pod_Rep2_ATH1 GSM133820: Yang_1-5_young-pod_Rep3_ATH1 GSM133821: Yang_1-6_old-pod_Rep3_ATH1 85: GSE5734 record: Effect of mycotoxin treatment on gene expression of wild-type and an altered sensitivity mutant [Arabidopsis thaliana] Summary: Fungal secondary metabolites can not only cause toxic effects in animals and humans, but also serve as virulence factors of the producing fungi for causing plant diseases.Thus, the severity of plant diseases associated with mycotoxins depend on the sensitivity towards the toxin. In previous experiments, we have evaluated the phytotoxic effect ofa mycotoxin on root growth of Arabidopsis wild-type and mutant seedlings. Mycotoxin treatment of a new conditional root expansion mutant partially restores the expansion phenotype (JE100; Werner et al., unpublished). AIM: This experiment aims to identify genes, in early and later phases after mycotoxin treatment in wild-type and mutant seedlings. EXPERIMENTAL PLAN: Eight Affymetrix chips are needed for this experiment. RNA preparation will be provided from wild-type, accession Columbia, and mutant seedlings after different time points of mycotoxin treatment. Samples: 8 GSM133800: Werner_1-1_wildtype-2hr-control(c2s)_Rep1_ATH1 GSM133801: Werner_1-2_wildtype-24hr-control(c4s)_Rep1_ATH1 GSM133802: Werner_1-3_mutant-2hr-control(j2s)_Rep1_ATH1 GSM133803: Werner_1-4_mutant-24hr-control(j4s)_Rep1_ATH1 GSM133804: Werner_1-5_wildtype-2hr-zearalenone(c2t)_Rep1_ATH1 GSM133805: Werner_1-6_wildtype-24hr-zearalenone(c4t)_Rep1_ATH1 GSM133806: Werner_1-7_mutant-2hr-zearalenone(j2t)_Rep1_ATH1 GSM133807: Werner_1-8_mutant-24hr-zearalenone(j4t)_Rep1_ATH1 86: GSE5686 record: AtGenExpress: Pathogen Series: Response to Erysiphe orontii infection [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 48 GSM133069: JD AT+EO COL WT 02D INFECTED GSM133070: JD AT+EO COL WT 02D UNINFECTED GSM133071: JD AT+EO COL WT 03D INFECTED GSM133072: JD AT+EO COL WT 03D UNINFECTED GSM133073: JD AT+EO COL WT 04D INFECTED GSM133074: JD AT+EO COL WT 04D UNINFECTED GSM133075: JD AT+EO COL WT 05D INFECTED GSM133076: JD AT+EO COL WT 05D UNINFECTED GSM133077: JD AT+EO COL WT 06H INFECTED GSM133078: JD AT+EO COL WT 06H UNINFECTED GSM133079: JD AT+EO COL WT 12H INFECTED GSM133080: JD AT+EO COL WT 12H UNINFECTED GSM133081: JD AT+EO COL WT 18H INFECTED GSM133082: JD AT+EO COL WT 18H UNINFECTED GSM133083: JD AT+EO COL WT 24H INFECTED GSM133084: JD AT+EO COL WT 24H UNINFECTED GSM133085: JD AT+EO COL WT EXP2 02D INFECTED GSM133086: JD AT+EO COL WT EXP2 02D UNINFECTED GSM133087: JD AT+EO COL WT EXP2 03D INFECTED GSM133088: JD AT+EO COL WT EXP2 03D UNINFECTED GSM133089: JD AT+EO COL WT EXP2 04D INFECTED GSM133090: JD AT+EO COL WT EXP2 04D UNINFECTED GSM133091: JD AT+EO COL WT EXP2 05D INFECTED GSM133092: JD AT+EO COL WT EXP2 05D UNINFECTED GSM133093: JD AT+EO COL WT EXP2 06H INFECTED GSM133094: JD AT+EO COL WT EXP2 06H UNINFECTED GSM133095: JD AT+EO COL WT EXP2 12H INFECTED GSM133096: JD AT+EO COL WT EXP2 12H UNINFECTED GSM133097: JD AT+EO COL WT EXP2 18H INFECTED GSM133098: JD AT+EO COL WT EXP2 18H UNINFECTED GSM133099: JD AT+EO COL WT EXP2 24H INFECTED GSM133100: JD AT+EO COL WT EXP2 24H UNINFECTED GSM133101: JD AT+EO TIME EXP3 EO INF 12H GSM133102: JD AT+EO TIME EXP3 EO INF 18H GSM133103: JD AT+EO TIME EXP3 EO INF 24H GSM133104: JD AT+EO TIME EXP3 EO INF 2D GSM133105: JD AT+EO TIME EXP3 EO INF 3D GSM133106: JD AT+EO TIME EXP3 EO INF 4D GSM133107: JD AT+EO TIME EXP3 EO INF 5D GSM133108: JD AT+EO TIME EXP3 EO INF 6H GSM133109: JD AT+EO TIME EXP3 UNINF 12H GSM133110: JD AT+EO TIME EXP3 UNINF 18H GSM133111: JD AT+EO TIME EXP3 UNINF 24H GSM133112: JD AT+EO TIME EXP3 UNINF 2D GSM133113: JD AT+EO TIME EXP3 UNINF 3D GSM133114: JD AT+EO TIME EXP3 UNINF 4D GSM133115: JD AT+EO TIME EXP3 UNINF 5D GSM133116: JD AT+EO TIME EXP3 UNINF 6H 87: GSE5684 record: AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 12 GSM133025: BC181-1 GSM133026: BC181-2 GSM133027: BC182-1 GSM133028: BC481-1 GSM133029: BC482-1 GSM133030: BC482-2 GSM133031: CT181-1 GSM133032: CT181-2 GSM133033: CT182-1 GSM133034: CT481-1 GSM133035: CT482-1 GSM133036: CT482-2 88: GSE5752 record: Expression Level Polymorphism Project (ELP) - Col-0 [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134340: St.Clair_1-1_289b_Col-0_0.02%-silwet_Rep1_ATH1 GSM134341: St.Clair_1-2_331_Col-0_0.02%-silwet_Rep2_ATH1 GSM134342: St.Clair_1-3_404_Col-0_0.02%-silwet_Rep3_ATH1 GSM134343: St.Clair_1-4_284b_Col-0_0.02%-silwet_Rep1_ATH1 GSM134344: St.Clair_1-5_325_Col-0_0.02%-silwet_Rep2_ATH1 GSM134345: St.Clair_1-6_398_Col-0_0.02%-silwet_Rep3_ATH1 GSM134346: St.Clair_1-7_273b_Col-0_0.02%-silwet_Rep1_ATH1 GSM134347: St.Clair_1-8_311_Col-0_0.02%-silwet_Rep2_ATH1 GSM134348: St.Clair_1-9_353_Col-0_0.02%-silwet_Rep3_ATH1 GSM134349: St.Clair_1-10_292b_Col-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134350: St.Clair_1-11_333_Col-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134351: St.Clair_1-12_407_Col-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134352: St.Clair_1-13_287b_Col-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134353: St.Clair_1-14_328_Col-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134354: St.Clair_1-15_400_Col-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134355: St.Clair_1-16_277b_Col-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134356: St.Clair_1-17_317_Col-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134357: St.Clair_1-18_357-2_Col-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 89: GSE5750 record: Growth of suspension-cultured cells [Arabidopsis thaliana] Summary: The growth of Arabidopsis cell cultures following their sub-culture into fresh media follows standard growth kinetics of a period of exponential increase associated with high rate of cell division, followed by a slowing of the rate of increase as cells approach stationary phase. For the analysis described here, MM2d cells were subcultured into fresh MSS-medium and samples were taken at day 1, day3, day 5 and day7. We have carried out transcriptional profiling analysis with the aim to follow growth stage specific gene expression during unperturbed growth using the near full genome ATH1 arrays (Menges et al., 2003). Journal Absract: (Plant Molecular Biology: 53, 2003) Plant cell suspension cultures are invaluable models for the study of cellular processes. Here we develop the recently described Arabidopsis suspension culture MM2d as a transcript profiling platform by means of Affymetrix ATH1 microarrays. Samples: 4 GSM134202: Murray_3-1_D1-GROWTH_Rep1_ATH1 GSM134204: Murray_3-2_D3-GROWTH_Rep1_ATH1 GSM134206: Murray_3-3_D5-GROWTH_Rep1_ATH1 GSM134208: Murray_3-4_D7-GROWTH_Rep1_ATH1 90: GSE5618 record: Comparative transcriptome analysis of wild type and two knockout alleles of At-CAMTA [Arabidopsis thaliana] Summary: Calcium has been shown to be an important signalling molecule in the transduction of abiotic stress signals in Arabidopsis thaliana. Alteration of the calcium signature through the use of inhibitors has been shown to result in changes in the expression of certain downstream abiotic stress-induced genes. However, the communication of this signal through specific calcium-sensitive intermediate molecules has remained poorly elucidated. Various candidate molecules exist and including calcinurin, calcium-dependent protein kinases and calmodulin. Recently, a screen of an Arabidopsis thaliana cDNA expression library with calmodulin resulted in the isolation of the protein designated calmodulin-binding transcriptional activator or AtCAMTA that may function as one of these calcium-sensitive intermediate molecules. Samples: 4 GSM131217: Scrase-Field_1-1_wassilewskija-wildtype_Rep1_ATH1 GSM131218: Scrase-Field_1-2_wassilewskija-camta1.1-knockout_Rep1_ATH1 GSM131219: Scrase-Field_1-3_Columbia-wildtype_Rep1_ATH1 GSM131220: Scrase-Field_1-4_Columbia-camta1.2-knockout_Rep1_ATH1 91: GSE5740 record: Polycomb Binding Protein [Arabidopsis thaliana] Summary: We have identified a gene encoding apolycomb-chromo domain binding protein. Complete knockout of these plants do not lead to a phenotype, but a reduction of gene expression in RNAi line produces a defined phenotype. This argues in favour of a compensation mechanism that is switched on once the concentration of the gene reaches a control level.The aim of the experiment is to search for such compensatory factors that are up-regulated in the knockout line. Experimenter name = Katharine Cain Experimenter phone = 01133433146 Experimenter department = University of Leeds Experimenter address = University of Leeds Experimenter address = Clarendon Way Experimenter address = Leeds Experimenter zip/postal_code = LS29JT Experimenter country = UK Samples: 4 GSM133866: Cain_1-1_WT1_Rep1_ATH1 GSM133867: Cain_1-3_CDB1-Knockout_Rep1_ATH1 GSM133868: Cain_1-2_WT1_Rep2_ATH1 GSM133869: Cain_1-4_CDB1-Knockout_Rep2_ATH1 92: GSE5739 record: Comparison of CATMA, Affymetrix and Agilent arrays [Arabidopsis thaliana] Summary: Transcript profiling is crucial to study biological systems and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the characteristics of the CATMA microarray designed for Arabidopsis thaliana transcriptome analysis, and compared it with two commercial platforms from Agilent and Affymetrix. The CATMA array consists of gene-specific sequence tags of 150 to 500 base pairs, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (TIGR release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled target derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. Samples: 8 GSM133858: Beynon_1-1-cat-SpikeMix1_Rep1_ATH1 GSM133859: Beynon_1-2-cat-SpikeMix2_Rep1_ATH1 GSM133860: Beynon_1-3-cat-SpikeMix3_Rep1_ATH1 GSM133861: Beynon_1-4-cat-SpikeMix4_Rep1_ATH1 GSM133862: Beynon_1-5-cat-SpikeMix5_Rep1_ATH1 GSM133863: Beynon_1-6-cat-SpikeMix6_Rep1_ATH1 GSM133864: Beynon_1-7-cat-SpikeMix7_Rep1_ATH1 GSM133865: Beynon_1-8-cat-ReferenceMix_Rep1_ATH1 93: GSE5738 record: Molecular bases of zinc tolerance and accumulation by Arabidopsis halleri [Arabidopsis thaliana Arabidopsis lyrata subsp. petraea Arabidopsis halleri] Summary: This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham). Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant. The objective of our programme is to identify: a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn), and b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response. Phase 1: Total of 24 chips: Material ready by May 2003. Samples: 24 GSM133834: Newbury_1-1_halleri-control-roots(HRO)_Rep1_ATH1 GSM133835: Newbury_1-3_Halleri-control-roots(HRO)_Rep1_ATH1 GSM133836: Newbury_1-4_Halleri-highZn-roots(HRH)_Rep1_ATH1 GSM133837: Newbury_1-7_Halleri-control-leaves(HLO)_Rep1_ATH1 GSM133838: Newbury_1-10_Halleri-highZn-leaves(HLH)_Rep1_ATH1 GSM133839: Newbury_1-13_Petraea-control-roots(PRO)_Rep1_ATH1 GSM133840: Newbury_1-16_Petraea-highZn-roots(PRH)_Rep1_ATH1 GSM133841: Newbury_1-18_Petraea-highZn-roots(PRH)_Rep3_ATH1 GSM133842: Newbury_1-19_Petraea-control-leaves(PLO)_Rep1_ATH1 GSM133843: Newbury_1-22_Petraea-highZn-leaves(PLH)_Rep1_ATH1 GSM133844: Newbury_1-2_halleri-control-roots(HRO)_Rep2_ATH1 GSM133845: Newbury_1-5_Halleri-highZn-roots(HRH)_Rep2_ATH1 GSM133846: Newbury_1-8_Halleri-control-leaves(HLO)_Rep2_ATH1 GSM133847: Newbury_1-11_Halleri-highZn-leavesHLH)_Rep2_ATH1 GSM133848: Newbury_1-14_Petraea-control-roots(PRO)_Rep2_ATH1 GSM133849: Newbury_1-17_Petraea-highZn-roots(PRH)_Rep2_ATH1 GSM133850: Newbury_1-20_Petraea-control-leaves(PLO)_Rep2_ATH1 GSM133851: Newbury_1-23_Petraea-highZn-leaves(PLH)_Rep2_ATH1 GSM133852: Newbury_1-6_Halleri-highZn-roots(HRH)_Rep3_ATH1 GSM133853: Newbury_1-9_Halleri-control-leaves(HLO)_Rep3_ATH1 GSM133854: Newbury_1-12_Halleri-highZn-leaves(HLH)_Rep3_ATH1 GSM133855: Newbury_1-15_Petraea-control-roots(PRO)_Rep3_ATH1 GSM133856: Newbury_1-21_Petraea-control-leaves(PLO)_Rep3_ATH1 GSM133857: Newbury_1-24_Petraea-highZn-leaves(PLH)_Rep3_ATH1 94: GSE5737 record: Carbohydrate- and redox-regulation of gene expression in a TPT mutant [Arabidopsis thaliana] Summary: The triose-phosphate/phosphate translocator (TPT) of the chloroplast inner envelope membrane mediates the counter-exchange of stromal triose phosphates derived from CO2 fixation with cytosolic phosphate, thus providing the cytosol with precursors for sucrose synthesis. We have isolated an Arabidopsis mutant (tpt-1) in which the gene encoding TPT is disrupted by a T-DNA insertion. During growth in low light tpt-1 plants are phenotypically normal, but in high light photosynthesis is inhibited and growth is retarded relative to wildtype. This mutant compensates for the absence of TPT by diverting photosynthate into starch which is hydrolysed and exported from the chloroplast as glucose that is subsequently phosphorylated by hexokinase. In low light the capacity of the pathway of starch synthesis is sufficient to accommodate the normal rate of CO2 fixation, but in high light it is unable to match the potential rate of CO2 fixation. Samples: 12 GSM133822: Walters_A-01-Kruger-WL1_REP1 GSM133823: Walters_A-02-Kruger-WL2_REP2 GSM133824: Walters_A-03-Kruger-WL3_REP3 GSM133825: Walters_A-04-Kruger-WH1_REP1 GSM133826: Walters_A-05-Kruger-WH2_REP2 GSM133827: Walters_A-06-Kruger-WH3_REP3 GSM133828: Walters_A-07-Kruger-ML1_REP1 GSM133829: Walters_A-08-Kruger-ML2_REP2 GSM133830: Walters_A-09-Kruger-ML3_REP3 GSM133831: Walters_A-10-Kruger-MH1_REP1 GSM133832: Walters_A-11-Kruger-MH2_REP2 GSM133833: Walters_A-12-Kruger-MH3_REP3 95: GSE5724 record: Plant gene expression associated with susceptibility to nematodes [Arabidopsis thaliana] Summary: Background Heterodera schachtii is an economically important plant parasitic nematode that forms a syncytium from a cell superficial to the formed vascular bundle by progressive recruitment of other cells into the structure. The pattern of plant gene expression changes dramatically inside the syncytium. The pathogen probably plays a major role in defining the plant response by choice of initial plant cell during precise behaviour in planta and/or by the secretions it releases. The modified plant cells enable a high feeding rate by the female nematode so enhancing its rate of development and subsequent daily egg production. Arabidopsis is widely used as a model plant to characterise molecular responses to nematodes (e.g. Sijmons et al., 1991 Plant J. 1:245-254.). A complete overview of the changes in plant gene expression when sedentary nematodes establish has not yet been gained using Arabidopsis or any other host plant. Samples: 2 GSM133717: Urwin_A-1-Urwin-Con_SLD GSM133718: Urwin_A-2-Urwin-Inf_SLD 96: GSE5723 record: IdentificationOf genes responsive to non-metabolised glucose analogs: approach to hexokinase-independent glucose sensing [Arabidopsis thaliana] Summary: It has been strongly argued that plant cells should have a means of sensing sugars at the cell surface, so that extracellular and intracellular sugars can be sensed separately and their metabolism coordinated (Lalonde et al., Plant Cell, 11, 707-26, 2000). There is good evidence for an intracellular hexokinase-dependent pathway of hexose sensing in plants, but very little evidence for a hexokinase-independent signalling pathway, such as that provided by SNF3 or RGT2 in yeast. Many papers on sugar sensing in plants cite work from two laboratories as evidence for hexokinase-independent hexose signalling in plants. The first is that in which cell-wall invertase and sucrose synthase genes were induced by treatment of a Chenopodium suspension culture with 30 mM 6-Deoxyglucose (6DOG) for 24 h (Roitsch et al., Plant Physiol 108, 285-294, 1995; Godt et al., J. Samples: 6 GSM133711: Villadsen_A-1-villa-zer_SLD GSM133712: Villadsen_A-2-villa-wat_SLD GSM133713: Villadsen_A-3-villa-glc_SLD GSM133714: Villadsen_A-4-villa-OMG_SLD GSM133715: Villadsen_A-5-villa-DOG_SLD GSM133716: Villadsen_A-6-villa-man_SLD 97: GSE5722 record: Functional Genomics of Ozone Stress in Arabidopsis. [Arabidopsis thaliana] Summary: Ozone is known to induce gene expression in plants. The roles of the induced genes and the molecular basis for the induction however largely remain to be elucidated. We will expose 2 week-old Arabidopsis seedlings to 200 ppb ozone for 1 h. RNA will be extracted from control and ozone-fumigated seedlings 3 h following the end of the fumigation period. The induction of the known anti-oxidant enzyme GST will be confirmed prior to submission of the RNA samples to GARNet. Changes in gene expression will be assessed by hybridising microarrays with fluorescently labelled cDNA prepared from control and ozone-fumigated seedlings. The role of selected genes will be inferred from their sequence and further established by over expression under the control of the 35S or cell-specific promoters and by searching for mutants among single transposon or T-DNA insertion collections. Samples: 6 GSM133705: Short_1-1_ozone_Rep1_ATH1 GSM133706: Short_1-2_control_Rep1_ATH1 GSM133707: Short_1-3_ozone_Rep2_ATH1 GSM133708: Short_1-5_ozone_Rep3_ATH1 GSM133709: Short_1-4_control_Rep2_ATH1 GSM133710: Short_1-6_control_Rep3_ATH1 98: GSE5688 record: AtGenExpress: Response to sulfate limitation [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 22 GSM133121: S0_12H_A GSM133122: S0_12H_B GSM133123: S0_24H_A GSM133124: S0_24H_B GSM133125: S0_2H_A GSM133126: S0_2H_B GSM133127: S0_4H_A GSM133128: S0_4H_B GSM133129: S0_8H_A GSM133130: S0_8H_B GSM133131: S1500_0H_A GSM133132: S1500_0H_B GSM133133: S1500_12H_A GSM133134: S1500_12H_B GSM133135: S1500_24H_A GSM133136: S1500_24H_B GSM133137: S1500_2H_A GSM133138: S1500_2H_B GSM133139: S1500_4H_A GSM133140: S1500_4H_B GSM133141: S1500_8H_A GSM133142: S1500_8H_B 99: GSE5687 record: AtGenExpress: Different temperature treatment of seeds [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 4 GSM133117: RIKEN-YAMAUCHI1A GSM133118: RIKEN-YAMAUCHI1B GSM133119: RIKEN-YAMAUCHI2A GSM133120: RIKEN-YAMAUCHI2B 100: GSE5757 record: Expression Level Polymorphism Project (ELP) - Kin-0 [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134430: St.Clair_1-55_269b_Kin-0_0.02%-silwet_Rep1_ATH1 GSM134431: St.Clair_1-56_319_Kin-0_0.02%-silwet_Rep2_ATH1 GSM134432: St.Clair_1-57_377_Kin-0_0.02%-silwet_Rep3_ATH1 GSM134433: St.Clair_1-58_281_Kin-0_0.02%-silwet_Rep1_ATH1 GSM134434: St.Clair_1-59_303_Kin-0_0.02%-silwet_Rep2_ATH1 GSM134435: St.Clair_1-60_365_Kin-0_0.02%-silwet_Rep3_ATH1 GSM134436: St.Clair_1-61_274_Kin-0_0.02%-silwet_Rep1_ATH1 GSM134437: St.Clair_1-62_309_Kin-0_0.02%-silwet_Rep2_ATH1 GSM134438: St.Clair_1-63_372_Kin-0_0.02%-silwet_Rep3_ATH1 GSM134439: St.Clair_1-64_270b_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134440: St.Clair_1-65_322_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134441: St.Clair_1-66_380_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134442: St.Clair_1-67_282_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134443: St.Clair_1-68_306_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134444: St.Clair_1-69_369_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134445: St.Clair_1-70_278_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134446: St.Clair_1-71_315_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134447: St.Clair_1-72_374_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 101: GSE5756 record: Expression Level Polymorphism Project (ELP) - Van-0 [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134412: St.Clair_1-109_347_Van-0_0.02%-silwet_Rep1_ATH1 GSM134413: St.Clair_1-110_375_Van-0_0.02%-silwet_Rep2_ATH1 GSM134414: St.Clair_1-111_430_Van-0_0.02%-silwet_Rep3_ATH1 GSM134415: St.Clair_1-112_327_Van-0_0.02%-silwet_Rep1_ATH1 GSM134416: St.Clair_1-113_381_Van-0_0.02%-silwet_Rep2_ATH1 GSM134417: St.Clair_1-114_438_Van-0_0.02%-silwet_Rep3_ATH1 GSM134418: St.Clair_1-115_312_Van-0_0.02%-silwet_Rep1_ATH1 GSM134419: St.Clair_1-116_387_Van-0_0.02%-silwet_Rep2_ATH1 GSM134420: St.Clair_1-117_450_Van-0_0.02%-silwet_Rep3_ATH1 GSM134421: St.Clair_1-118_348_Van-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134422: St.Clair_1-119_378_Van-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134423: St.Clair_1-120_434_Van-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134424: St.Clair_1-121_330_Van-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134425: St.Clair_1-122_384_Van-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134426: St.Clair_1-123_444_Van-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134427: St.Clair_1-124_318_Van-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134428: St.Clair_1-125_390_Van-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134429: St.Clair_1-126_455_Van-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 102: GSE5755 record: Expression Level Polymorphism Project (ELP) - Tsu-1 [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134394: St.Clair_1-91_267b_Tsu-1_0.02%-silwet_Rep1_ATH1 GSM134395: St.Clair_1-92_321_Tsu-1_0.02%-silwet_Rep2_ATH1 GSM134396: St.Clair_1-93_349_Tsu-1_0.02%-silwet_Rep3_ATH1 GSM134397: St.Clair_1-94_271_Tsu-1_0.02%-silwet_Rep1_ATH1 GSM134398: St.Clair_1-95_301_Tsu-1_0.02%-silwet_Rep2_ATH1 GSM134399: St.Clair_1-96_351_Tsu-1_0.02%-silwet_Rep3_ATH1 GSM134400: St.Clair_1-97_296_Tsu-1_0.02%-silwet_Rep1_ATH1 GSM134401: St.Clair_1-98_307_Tsu-1_0.02%-silwet_Rep2_ATH1 GSM134402: St.Clair_1-99_354_Tsu-1_0.02%-silwet_Rep3_ATH1 GSM134403: St.Clair_1-100_268b_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134404: St.Clair_1-101_324_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134405: St.Clair_1-102_350_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134406: St.Clair_1-103_272_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134407: St.Clair_1-104_304_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134408: St.Clair_1-105_352_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134409: St.Clair_1-106_298_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134410: St.Clair_1-107_313_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134411: St.Clair_1-108_358_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 103: GSE5754 record: Expression Level Polymorphism Project (ELP) - Est [Arabidopsis thaliana] Summary: This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Samples: 18 GSM134376: St.Clair_1-37_290_Est_0.02%-silwet_Rep1_ATH1 GSM134377: St.Clair_1-38_332_Est_0.02%-silwet_Rep2_ATH1 GSM134378: St.Clair_1-39_394_Est_0.02%-silwet_Rep3_ATH1 GSM134379: St.Clair_1-40_285_Est_0.02%-silwet_Rep1_ATH1 GSM134380: St.Clair_1-41_326b_Est_0.02%-silwet_Rep2_ATH1 GSM134381: St.Clair_1-42_383_Est_0.02%-silwet_Rep3_ATH1 GSM134382: St.Clair_1-43_275b_Est_0.02%-silwet_Rep1_ATH1 GSM134383: St.Clair_1-44_310_Est_0.02%-silwet_Rep2_ATH1 GSM134384: St.Clair_1-45_388_Est_0.02%-silwet_Rep3_ATH1 GSM134385: St.Clair_1-46_293_Est_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134386: St.Clair_1-47_334_Est_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134387: St.Clair_1-48_397_Est_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134388: St.Clair_1-49_288c_Est_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134389: St.Clair_1-50_329_Est_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134390: St.Clair_1-51_386_Est_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 GSM134391: St.Clair_1-52_279b_Est_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1 GSM134392: St.Clair_1-53_316_Est_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1 GSM134393: St.Clair_1-54_391_Est_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1 104: GSE5640 record: Growth promotion of Arabidopsis by Trichoderma hamatum [Arabidopsis thaliana] Summary: Trichoderma spp. are ubiquitous soil-borne ascomycetous fungi that have been used widely in the biological control of plant diseases. Certain strains also exhibit growth promotion of plants, but the mechanism for this phenomenon has not yet been elucidated. We have recently identified an isolate of T. hamatum that causes significant increases in the development of Arabidopsis root systems. The aim of this work is to elucidate the mechanism of root growth promotion. One approach is to analyse the transcriptome of plants grown in the presence and absence of the fungus. Experimenter name = Christopher Thornton Experimenter phone = 01392 264653 / 01392 264689 Experimenter department = Washington Singer Lab Experimenter address = School of Biological and Chemical Sciences Experimenter address =. Samples: 2 GSM131841: Thornton_1-1_Control_Rep1_ATH1 GSM131842: Thornton_1-2_Col+trichoderma_Rep1_ATH1 105: GSE5639 record: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Controls) [Arabidopsis thaliana] Summary: We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC. The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways. The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. Samples: 8 GSM131829: Quick_A1_1-0hr_Rep1_ATH1 GSM131830: Quick_A26_5-0hr_Rep1_ATH1 GSM131831: Quick_A27_0-0hr_Rep2_ATH1 GSM131832: Quick_A52_5-0hr_Rep2_ATH1 GSM131833: Quick_A53_0-0hr_Rep3_ATH1 GSM131834: Quick_A78_5-0hr_Rep3_ATH1 GSM131835: Quick_A79_0-0hr_Rep4_ATH1 GSM131836: Quick_A104_5-0hr_Rep4_ATH1 106: GSE5638 record: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 3: Ambient CO2 and Low Light) [Arabidopsis thaliana] Summary: We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC. The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways. The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. Samples: 28 GSM131801: Quick_A4_3-2hr_Rep1_ATH1 GSM131802: Quick_A8_3-4hr-Rep1_ATH1 GSM131803: Quick_A9_3-4hr-Rep1_ATH1 GSM131804: Quick_A12_3-12hr_Rep1_ATH1 GSM131805: Quick_A16_3-24hr_Rep1_ATH1 GSM131806: Quick_A17_3-24hr_Rep1_ATH1 GSM131807: Quick_A20_3-48hr_Rep1_ATH1 GSM131808: Quick_A24_3-96hr_Rep1_ATH1 GSM131809: Quick_A30_3-2hr_Rep2_ATH1 GSM131810: Quick_A34_3-4hr-Rep2_ATH1 GSM131811: Quick_A38_3-12hr_Rep2_ATH1 GSM131812: Quick_A42_3-24hr_Rep2_ATH1 GSM131813: Quick_A46_3-48hr_Rep2_ATH1 GSM131814: Quick_A50_3-96hr_Rep2_ATH1 GSM131815: Quick_A56_3-2hr_Rep3_ATH1 GSM131816: Quick_A60_3-4hr-Rep3_ATH1 GSM131817: Quick_A64_3-12hr_Rep3_ATH1 GSM131818: Quick_A68_3-24hr_Rep3_ATH1 GSM131819: Quick_A72_3-48hr_Rep3_ATH1 GSM131820: Quick_A76_3-96hr_Rep3_ATH1 GSM131821: Quick_A82_3-2hr_Rep4_ATH1 GSM131822: Quick_A86_3-4hr-Rep4_ATH1 GSM131823: Quick_A90_3-12hr_Rep4_ATH1 GSM131824: Quick_A94_3-24hr_Rep4_ATH1 GSM131825: Quick_A98_3-48hr_Rep4_ATH1 GSM131826: Quick_A102_3-96hr_Rep4_ATH1 GSM131827: Quick_A107_3-24hr_Rep1m_ATH1 GSM131828: Quick_A111_3-24hr_Rep2m_ATH1 107: GSE5637 record: Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 2: Elevated CO2 and Ambient Light) [Arabidopsis thaliana] Summary: We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC. The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways. The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. Samples: 26 GSM131775: Quick_A3_2-2hr_Rep1_ATH1 GSM131776: Quick_A7_2-4hr-Rep1_ATH1 GSM131777: Quick_A11_2-12hr_Rep1_ATH1 GSM131778: Quick_A15_2-24hr_Rep1_ATH1 GSM131779: Quick_A19_2-48hr_Rep1_ATH1 GSM131780: Quick_A23_2-96hr_Rep1_ATH1 GSM131781: Quick_A29_2-2hr_Rep2_ATH1 GSM131782: Quick_A33_2-4hr-Rep2_ATH1 GSM131783: Quick_A37_2-12hr_Rep2_ATH1 GSM131784: Quick_A41_2-24hr_Rep2_ATH1 GSM131785: Quick_A45_2-48hr_Rep2_ATH1 GSM131786: Quick_A49_2-96hr_Rep2_ATH1 GSM131787: Quick_A55_2-2hr_Rep3_ATH1 GSM131788: Quick_A59_2-4hr-Rep3_ATH1 GSM131789: Quick_A63_2-12hr_Rep3_ATH1 GSM131790: Quick_A67_2-24hr_Rep3_ATH1 GSM131791: Quick_A71_2-48hr_Rep3_ATH1 GSM131792: Quick_A75_2-96hr_Rep3_ATH1 GSM131793: Quick_A81_2-2hr_Rep4_ATH1 GSM131794: Quick_A85_2-4hr-Rep4_ATH1 GSM131795: Quick_A89_2-12hr_Rep4_ATH1 GSM131796: Quick_A93_2-24hr_Rep4_ATH1 GSM131797: Quick_A97_2-48hr_Rep4_ATH1 GSM131798: Quick_A101_2-96hr_Rep4_ATH1 GSM131799: Quick_A106_2-24hr_Rep1m_ATH1 GSM131800: Quick_A110_2-24hr_Rep2m_ATH1 108: GSE5623 record: AtGenExpress: Stress Treatments (Salt stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 24 GSM131307: AtGen_6-3111_Saltstress-Shoots-0.5h_Rep1 GSM131308: AtGen_6-3112_Saltstress-Shoots-0.5h_Rep2 GSM131309: AtGen_6-3121_Saltstress-Roots-0.5h_Rep1 GSM131310: AtGen_6-3122_Saltstress-Roots-0.5h_Rep2 GSM131311: AtGen_6-3211_Saltstress-Shoots-1.0h_Rep1 GSM131312: AtGen_6-3212_Saltstress-Shoots-1.0h_Rep2 GSM131313: AtGen_6-3221_Saltstress-Roots-1.0h_Rep1 GSM131314: AtGen_6-3222_Saltstress-Roots-1.0h_Rep2 GSM131315: AtGen_6-3311_Saltstress-Shoots-3.0h_Rep1 GSM131316: AtGen_6-3312_Saltstress-Shoots-3.0h_Rep2 GSM131317: AtGen_6-3321_Saltstress-Roots-3.0h_Rep1 GSM131318: AtGen_6-3322_Saltstress-Roots-3.0h_Rep2 GSM131319: AtGen_6-3411_Saltstress-Shoots-6.0h_Rep1 GSM131320: AtGen_6-3412_Saltstress-Shoots-6.0h_Rep2 GSM131321: AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSM131322: AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSM131323: AtGen_6-3511_Saltstress-Shoots-12.0h_Rep1 GSM131324: AtGen_6-3512_Saltstress-Shoots-12.0h_Rep2 GSM131325: AtGen_6-3521_Saltstress-Roots-12.0h_Rep1 GSM131326: AtGen_6-3522_Saltstress-Roots-12.0h_Rep2 GSM131327: AtGen_6-3611_Saltstress-Shoots-24.0h_Rep1 GSM131328: AtGen_6-3612_Saltstress-Shoots-24.0h_Rep2 GSM131329: AtGen_6-3621_Saltstress-Roots-24.0h_Rep1 GSM131330: AtGen_6-3622_Saltstress-Roots-24.0h_Rep2 109: GSE5622 record: AtGenExpress: Stress Treatments (Osmotic stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 24 GSM131283: AtGen_6-2111_Osmoticstress-Shoots-0.5h_Rep1 GSM131284: AtGen_6-2112_Osmoticstress-Shoots-0.5h_Rep2 GSM131285: AtGen_6-2121_Osmoticstress-Roots-0.5h_Rep1 GSM131286: AtGen_6-2122_Osmoticstress-Roots-0.5h_Rep2 GSM131287: AtGen_6-2211_Osmoticstress-Shoots-1.0h_Rep1 GSM131288: AtGen_6-2212_Osmoticstress-Shoots-1.0h_Rep2 GSM131289: AtGen_6-2221_Osmoticstress-Roots-1.0h_Rep1 GSM131290: AtGen_6-2222_Osmoticstress-Roots-1.0h_Rep2 GSM131291: AtGen_6-2311_Osmoticstress-Shoots-3.0h_Rep1 GSM131292: AtGen_6-2312_Osmoticstress-Shoots-3.0h_Rep2 GSM131293: AtGen_6-2321_Osmoticstress-Roots-3.0h_Rep1 GSM131294: AtGen_6-2322_Osmoticstress-Roots-3.0h_Rep2 GSM131295: AtGen_6-2411_Osmoticstress-Shoots-6.0h_Rep1 GSM131296: AtGen_6-2412_Osmoticstress-Shoots-6.0h_Rep2 GSM131297: AtGen_6-2421_Osmoticstress-Roots-6.0h_Rep1 GSM131298: AtGen_6-2422_Osmoticstress-Roots-6.0h_Rep2 GSM131299: AtGen_6-2511_Osmoticstress-Shoots-12.0h_Rep1 GSM131300: AtGen_6-2512_Osmoticstress-Shoots-12.0h_Rep2 GSM131301: AtGen_6-2521_Osmoticstress-Roots-12.0h_Rep1 GSM131302: AtGen_6-2522_Osmoticstress-Roots-12.0h_Rep2 GSM131303: AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1 GSM131304: AtGen_6-2612_Osmoticstress-Shoots-24.0h_Rep2 GSM131305: AtGen_6-2621_Osmoticstress-Roots-24.0h_Rep1 GSM131306: AtGen_6-2622_Osmoticstress-Roots-24.0h_Rep2 110: GSE5621 record: AtGenExpress: Stress Treatments (Cold stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 24 GSM131259: AtGen_6-1111_Cold(4°C)-Shoots-0.5h_Rep1 GSM131260: AtGen_6-1112_Cold(4°C)-Shoots-0.5h_Rep2 GSM131261: AtGen_6-1121_Cold(4°C)-Roots-0.5h_Rep1 GSM131262: AtGen_6-1122_Cold(4°C)-Roots-0.5h_Rep2 GSM131263: AtGen_6-1211_Cold(4°C)-Shoots-1.0h_Rep1 GSM131264: AtGen_6-1212_Cold(4°C)-Shoots-1.0h_Rep2 GSM131265: AtGen_6-1221_Cold(4°C)-Roots-1.0h_Rep1 GSM131266: AtGen_6-1222_Cold(4°C)-Roots-1.0h_Rep2 GSM131267: AtGen_6-1311_Cold(4°C)-Shoots-3.0h_Rep1 GSM131268: AtGen_6-1312_Cold(4°C)-Shoots-3.0h_Rep2 GSM131269: AtGen_6-1321_Cold(4°C)-Roots-3.0h_Rep1 GSM131270: AtGen_6-1322_Cold(4°C)-Roots-3.0h_Rep2 GSM131271: AtGen_6-1411_Cold(4°C)-Shoots-6.0h_Rep1 GSM131272: AtGen_6-1412_Cold(4°C)-Shoots-6.0h_Rep2 GSM131273: AtGen_6-1421_Cold(4°C)-Roots-6.0h_Rep1 GSM131274: AtGen_6-1422_Cold(4°C)-Roots-6.0h_Rep2 GSM131275: AtGen_6-1511_Cold(4°C)-Shoots-12.0h_Rep1 GSM131276: AtGen_6-1512_Cold(4°C)-Shoots-12.0h_Rep2 GSM131277: AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1 GSM131278: AtGen_6-1522_Cold(4°C)-Roots-12.0h_Rep2 GSM131279: AtGen_6-1611_Cold(4°C)-Shoots-24.0h_Rep1 GSM131280: AtGen_6-1612_Cold(4°C)-Shoots-24.0h_Rep2 GSM131281: AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1 GSM131282: AtGen_6-1622_Cold(4°C)-Roots-24.0h_Rep2 111: GSE5620 record: AtGenExpress: Stress Treatments (Control plants) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 36 GSM131223: AtGen_6-0011_Control-Shoots-0h_Rep1 GSM131224: AtGen_6-0012_Control-Shoots-0h_Rep2 GSM131225: AtGen_6-0021_Control-Roots-0h_Rep1 GSM131226: AtGen_6-0022_Control-Roots-0h_Rep2 GSM131227: AtGen_6-0711_Control-Shoots-0.25h_Rep1 GSM131228: AtGen_6-0712_Control-Shoots-0.25h_Rep2 GSM131229: AtGen_6-0721_Control-Roots-0.25h_Rep1 GSM131230: AtGen_6-0722_Control-Roots-0.25h_Rep2 GSM131231: AtGen_6-0111_Control-Shoots-0.5h_Rep1 GSM131232: AtGen_6-0112_Control-Shoots-0.5h_Rep2 GSM131233: AtGen_6-0121_Control-Roots-0.5h_Rep1 GSM131234: AtGen_6-0122_Control-Roots-0.5h_Rep2 GSM131235: AtGen_6-0211_Control-Shoots-1.0h_Rep1 GSM131236: AtGen_6-0212_Control-Shoots-1.0h_Rep2 GSM131237: AtGen_6-0221_Control-Roots-1.0h_Rep1 GSM131238: AtGen_6-0222_Control-Roots-1.0h_Rep2 GSM131239: AtGen_6-0311_Control-Shoots-3.0h_Rep1 GSM131240: AtGen_6-0312_Control-Shoots-3.0h_Rep2 GSM131241: AtGen_6-0321_Control-Roots-3.0h_Rep1 GSM131242: AtGen_6-0322_Control-Roots-3.0h_Rep2 GSM131243: AtGen_6-0811_Control-Shoots-4.0h_Rep1 GSM131244: AtGen_6-0812_Control-Shoots-4.0h_Rep2 GSM131245: AtGen_6-0821_Control-Roots-4.0h_Rep1 GSM131246: AtGen_6-0822_Control-Roots-4.0h_Rep2 GSM131247: AtGen_6-0411_Control-Shoots-6.0h_Rep1 GSM131248: AtGen_6-0412_Control-Shoots-6.0h_Rep2 GSM131249: AtGen_6-0421_Control-Roots-6.0h_Rep1 GSM131250: AtGen_6-0422_Control-Roots-6.0h_Rep2 GSM131251: AtGen_6-0511_Control-Shoots-12.0h_Rep1 GSM131252: AtGen_6-0512_Control-Shoots-12.0h_Rep2 GSM131253: AtGen_6-0521_Control-Roots-12.0h_Rep1 GSM131254: AtGen_6-0522_Control-Roots-12.0h_Rep2 GSM131255: AtGen_6-0611_Control-Shoots-24.0h_Rep1 GSM131256: AtGen_6-0612_Control-Shoots-24.0h_Rep2 GSM131257: AtGen_6-0621_Control-Roots-24.0h_Rep1 GSM131258: AtGen_6-0622_Control-Roots-24.0h_Rep2 112: GSE5698 record: AtGenExpress: Cytokinin treatment of seedlings [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 12 GSM133285: NO.10 GSM133286: NO.11 GSM133287: NO.12 GSM133288: NO.19-2 GSM133289: NO.20-2 GSM133290: NO.21-2 GSM133291: NO.28 GSM133292: NO.29 GSM133293: NO.30 GSM133294: NO.31 GSM133295: NO.32 GSM133296: NO.33 113: GSE5697 record: AtGenExpress: Comparison of plant hormone-related mutants [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 8 GSM133277: RIKEN-GODA1A-M GSM133278: RIKEN-GODA1B-M GSM133279: RIKEN-GODA2A-M GSM133280: RIKEN-GODA2B-M GSM133281: RIKEN-GODA3A-M GSM133282: RIKEN-GODA3B-M GSM133283: RIKEN-GODA4A-M GSM133284: RIKEN-GODA4B-M 114: GSE5696 record: AtGenExpress: Effect of brassinosteroids in seedlings [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 26 GSM133251: RIKEN-GODA10A-6 GSM133252: RIKEN-GODA10B-6 GSM133253: RIKEN-GODA11A-6 GSM133254: RIKEN-GODA11B-6 GSM133255: RIKEN-GODA12A-6 GSM133256: RIKEN-GODA12B-6 GSM133257: RIKEN-GODA13A-6 GSM133258: RIKEN-GODA13B-6 GSM133259: RIKEN-GODA1A-6 GSM133260: RIKEN-GODA1B-6 GSM133261: RIKEN-GODA2A-6 GSM133262: RIKEN-GODA2B-6 GSM133263: RIKEN-GODA3A-6 GSM133264: RIKEN-GODA3B-6 GSM133265: RIKEN-GODA4A-6 GSM133266: RIKEN-GODA4B-6 GSM133267: RIKEN-GODA5A-6 GSM133268: RIKEN-GODA5B-6 GSM133269: RIKEN-GODA6A-6 GSM133270: RIKEN-GODA6B-6 GSM133271: RIKEN-GODA7A-6 GSM133272: RIKEN-GODA7B-6 GSM133273: RIKEN-GODA8A-6 GSM133274: RIKEN-GODA8B-6 GSM133275: RIKEN-GODA9A-6 GSM133276: RIKEN-GODA9B-6 115: GSE5615 record: AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC) The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 42 GSM131109: AtGen_B-37_3-2-4_REP3_ATH1 GSM131110: AtGen_B-38_3-3-4_REP3_ATH1 GSM131111: AtGen_B-39_3-4-4_REP3_ATH1 GSM131112: AtGen_B-40_3-5-4_REP3_ATH1 GSM131113: AtGen_B-41_3-6-4_REP3_ATH1 GSM131114: AtGen_B-42_3-7-4_REP3_ATH1 GSM131115: AtGen_B-1_1-1-1_REP_1_ATH1 GSM131116: AtGen_B-2_1-2-1_REP_1_ATH1 GSM131117: AtGen_B-3_1-3-1_REP_1_ATH1 GSM131118: AtGen_B-4_1-4-1_REP_1_ATH1 GSM131119: AtGen_B-5_1-5-1_REP_1_ATH1 GSM131120: AtGen_B-6_1-6-1_REP_1_ATH1 GSM131121: AtGen_B-7_1-7-1_REP_1_ATH1 GSM131122: AtGen_B-8_1-1-4_REP_1_ATH1 GSM131123: AtGen_B-9_1-2-4_REP_1_ATH1 GSM131124: AtGen_B-10_1-3-4_REP1_ATH1 GSM131125: AtGen_B-11_1-4-4_REP1_ATH1 GSM131126: AtGen_B-12_1-5-4_REP1_ATH1 GSM131127: AtGen_B-13_1-6-4_REP1_ATH1 GSM131128: AtGen_B-14_1-7-4_REP1_ATH1 GSM131129: AtGen_B-15_2-1-1_REP2_ATH1 GSM131130: AtGen_B-16_2-2-1_REP2_ATH1 GSM131131: AtGen_B-17_2-3-1_REP2_ATH1 GSM131132: AtGen_B-18_2-4-1_REP2_ATH1 GSM131133: AtGen_B-19_2-5-1_REP2_ATH1 GSM131134: AtGen_B-20_2-6-1_REP2_ATH1 GSM131135: AtGen_B-21_2-7-1_REP2_ATH1 GSM131136: AtGen_B-22_2-1-4_REP2_ATH1 GSM131137: AtGen_B-23_2-2-4_REP2_ATH1 GSM131138: AtGen_B-24_2-3-4_REP2_ATH1 GSM131139: AtGen_B-25_2-4-4_REP2_ATH1 GSM131140: AtGen_B-26_2-5-4_REP2_ATH1 GSM131141: AtGen_B-27_2-6-4_REP2_ATH1 GSM131142: AtGen_B-28_2-7-4_REP2_ATH1 GSM131143: AtGen_B-29_3-1-1_REP3_ATH1 GSM131144: AtGen_B-30_3-2-1_REP3_ATH1 GSM131145: AtGen_B-31_3-3-1_REP3_ATH1 GSM131146: AtGen_B-32_3-4-1_REP3_ATH1 GSM131147: AtGen_B-33_3-5-1_REP3_ATH1 GSM131148: AtGen_B-34_3-6-1_REP3_ATH1 GSM131149: AtGen_B-35_3-7-1_REP3_ATH1 GSM131150: AtGen_B-36_3-1-4_REP3_ATH1 116: GSE5614 record: Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study) [Arabidopsis thaliana] Summary: The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. Samples: 6 GSM131103: Broadley_1-1_A1-Bo+P-nutrient-replete_Rep1_ATH1 GSM131104: Broadley_1-2_A2-Bo-P-phosphate-starved_Rep1_ATH1 GSM131105: Broadley_1-3_A3-Bo-P2-phosphate-starved_Rep2_ATH1 GSM131106: Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1 GSM131107: Broadley_1-5_A5-Bo+P2-nutrient-replete_Rep2_ATH1 GSM131108: Broadley_1-6_A6-Bo+P3-nutrient-replete_Rep3_ATH1 117: GSE5613 record: Newbury: Molecular bases of zinc tolerance and accumulation by Arabidopsis halleri [Arabidopsis thaliana Arabidopsis halleri] Summary: This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham). Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant. The objective of our programme is to identify a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn) and b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response. Phase 1: Total of 24 chips: Material ready by May 2003 The results will a) tell us how effectively material derived from other Arabidopsis species hybridises to the chips, and b) identify genes that are differentially expressed in the two species in the presence and absence of Zn stress (thus providing initial lists of genes that may be responsible for Zn tolerance or accumulation- but see phase 2)· A. Samples: 24 GSM131079: Newbury_2-1_non-acc-bulk-control-root(NRO)_Rep1_ATH1 GSM131080: Newbury_2-2_non-acc-bulk-control-root(NRO)_Rep2_ATH1 GSM131081: Newbury_2-3_non-acc-bulk-control-root(NRO)_Rep3_ATH1 GSM131082: Newbury_2-4_non-acc-bulk-highZn-root(NRH)_Rep1_ATH1 GSM131083: Newbury_2-5_non-acc-bulk-highZn-root(NRH)_Rep2_ATH1 GSM131084: Newbury_2-6_non-acc-bulk-highZn-root(NRH)_Rep3_ATH1 GSM131085: Newbury_2-7_non-acc-bulk-control-leaf(NLO)_Rep1_ATH1 GSM131086: Newbury_2-8_non-acc-bulk-control-leaf(NLO)_Rep2_ATH1 GSM131087: Newbury_2-9_non-acc-bulk-control-leaf(NLO)_Rep3_ATH1 GSM131088: Newbury_2-10_non-acc-bulk-highZn-leaf(NLH)_Rep1_ATH1 GSM131089: Newbury_2-11_non-acc-bulk-highZn-leaf(NLH)_Rep2_ATH1 GSM131090: Newbury_2-12_non-acc-bulk-highZn-leaf(NLH)_Rep3_ATH1 GSM131091: Newbury_2-13_acc-bulk-control-root(ARO)_Rep1_ATH1 GSM131092: Newbury_2-14_acc-bulk-control-root(ARO)_Rep2_ATH1 GSM131093: Newbury_2-15_acc-bulk-control-root(ARO)_Rep3_ATH1 GSM131094: Newbury_2-16_acc-bulk-highZn-root(ARH)_Rep1_ATH1 GSM131095: Newbury_2-17_acc-bulk-highZn-root(ARH)_Rep2_ATH1 GSM131096: Newbury_2-18_acc-bulk-highZn-root(ARH)_Rep3_ATH1 GSM131097: Newbury_2-19_acc-bulk-control-leaf(ALO)_Rep1_ATH1 GSM131098: Newbury_2-20_acc-bulk-control-leaf(ALO)_Rep2_ATH1 GSM131099: Newbury_2-21_acc-bulk-control-leaf(ALO)_Rep3_ATH1 GSM131100: Newbury_2-22_acc-bulk-highZn-leaf(ALH)_Rep1_ATH1 GSM131101: Newbury_2-23_acc-bulk-highZn-leaf(ALH)_Rep2_ATH1 GSM131102: Newbury_2-24_acc-bulk-highZn-leaf(ALH)_Rep3_ATH1 118: GSE5612 record: Circadian expression of genes: modelling the Arabidopsis circadian clock [Arabidopsis thaliana] Summary: Our aim is to study the circadian expression of genes to aid in our attempt of modelling the Arabidopsis circadian clock. Circadian microarray data have previously been published for plants after white light (WL)-dark cycles, using the 8k chip (Harmer et al. 2000). We intend to repeat this experiment using the 26k chips and are coordinating with Dr. Harmer, who is pursuing complementary experiments in UC Davis. Plants will be transferred to continuous WL after entrainment to 12h:12h light dark cycles. RNAs will be harvested every 4 hours over two days, with the same accession and sampling intervals used previously by Harmer et al. The two days of sampling provide internal replication. Our experience shows that this is the most economical design: it is easier to identify rhythms over a two-day timecourse than in two replicates of a single day. Samples: 13 GSM131066: Edwards_1-1_26hr_Rep1_ATH1 GSM131067: Edwards_1-2_30hr_Rep1_ATH1 GSM131068: Edwards_1-3_34hr_Rep1_ATH1 GSM131069: Edwards_1-4_38hr_Rep1_ATH1 GSM131070: Edwards_1-5_42hr_Rep1_ATH1 GSM131071: Edwards_1-6_46hr_Rep1_ATH1 GSM131072: Edwards_1-7_50hr_Rep1_ATH1 GSM131073: Edwards_1-8_54hr_Rep1_ATH1 GSM131074: Edwards_1-9_58hr_Rep1_ATH1 GSM131075: Edwards_1-10_62hr_Rep1_ATH1 GSM131076: Edwards_1-11_66hr_Rep1_ATH1 GSM131077: Edwards_1-12_70hr_Rep1_ATH1 GSM131078: Edwards_1-13_74hr_Rep1_ATH1 119: GSE6181 record: Assembly of the cell wall pectic matrix. [Arabidopsis thaliana] Summary: The primary cell walls of land plants are composed principally of a load bearing cellulose microfibril-hemicellulose network embedded in a matrix of pectic polysaccharides. The pectic matrix is multifunctional and in additional to a directly structural role it is central to many fundamental plant processes including cell expansion, defence and cell signalling. The sequencing of the Arabidopsis genome has revealed the massive investment made by plants in modulating the pectic matrix in response to local functional requirements but despite concerted biochemical-based efforts over many years none of the genes involved in pectin biosynthesis/pectic matrix assembly have so far been identified. The pectin matrix contains some of the most complex polysaccharides found in nature and based on linkage analysis it is known that at least 53 glycosyltransferases must be involved in its construction. Samples: 6 GSM142902: WW001_ATH1_A1-WILLA-CON GSM142903: WW001_ATH1_A2-WILLA-ISOX GSM142904: WW002_ATH1_A1-willa-CON-REP2 GSM142905: WW002_ATH1_A1-willa-CON-REP3 GSM142906: WW002_ATH1_A2-willa-ISOX-REP2 GSM142907: WW002_ATH1_A2-willa-ISOX-REP3 120: GSE5746 record: FRI FLC combos [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org).FRI FLC time series Experimenter name = Markus Schmid Experimenter phone = ++49-7071-601-1413 Experimenter fax = ++49-7071-601-1412 Experimenter department = Detlef Weigel Laboratory Germany Experimenter institute = Max-Planck-Institute for Developmental Biology Experimenter address = Dept. of Molecular Biology Experimenter address = Spemannstr. 37-39 Experimenter address = Tün Experimenter zip/postal_code = 72076 Experimenter country = Germnay Samples: 36 GSM133909: Weigel_2-1_CHIP-203-A_Rep1_ATH1 GSM133910: Weigel_2-2_CHIP-203-B_Rep2_ATH1 GSM133911: Weigel_2-3_CHIP-203-C_Rep3_ATH1 GSM133912: Weigel_2-4_CHIP-204-A_Rep1_ATH1 GSM133913: Weigel_2-5_CHIP-204-B_Rep2_ATH1 GSM133914: Weigel_2-6_CHIP-204-C_Rep3_ATH1 GSM133915: Weigel_2-7_CHIP-205-A_Rep1_ATH1 GSM133916: Weigel_2-8_CHIP-205-B_Rep2_ATH1 GSM133917: Weigel_2-9_CHIP-205-C_Rep3_ATH1 GSM133918: Weigel_2-10_CHIP-206-A_Rep1_ATH1 GSM133919: Weigel_2-11_CHIP-206-B_Rep2_ATH1 GSM133920: Weigel_2-12_CHIP-206-C_Rep3_ATH1 GSM133921: Weigel_2-13_CHIP-207-A_Rep1_ATH1 GSM133922: Weigel_2-14_CHIP-207-B_Rep2_ATH1 GSM133923: Weigel_2-15_CHIP-207-C_Rep3_ATH1 GSM133924: Weigel_2-16_CHIP-208-A_Rep1_ATH1 GSM133925: Weigel_2-17_CHIP-208-B_Rep2_ATH1 GSM133926: Weigel_2-18_CHIP-208-C_Rep3_ATH1 GSM133927: Weigel_2-19_CHIP-209-A_Rep1_ATH1 GSM133928: Weigel_2-20_CHIP-209-B_Rep2_ATH1 GSM133929: Weigel_2-21_CHIP-209-C_Rep3_ATH1 GSM133930: Weigel_2-22_CHIP-210-A_Rep1_ATH1 GSM133931: Weigel_2-23_CHIP-210-B_Rep2_ATH1 GSM133932: Weigel_2-24_CHIP-210-C_Rep3_ATH1 GSM133933: Weigel_2-25_CHIP-211-A_Rep1_ATH1 GSM133934: Weigel_2-26_CHIP-211-B_Rep2_ATH1 GSM133935: Weigel_2-27_CHIP-211-C_Rep3_ATH1 GSM133936: Weigel_2-28_CHIP-212-A_Rep1_ATH1 GSM133937: Weigel_2-29_CHIP-212-B_Rep2_ATH1 GSM133938: Weigel_2-30_CHIP-212-C_Rep3_ATH1 GSM133939: Weigel_2-31_CHIP-213-A_Rep1_ATH1 GSM133940: Weigel_2-32_CHIP-213-B_Rep2_ATH1 GSM133941: Weigel_2-33_CHIP-213-C_Rep3_ATH1 GSM133942: Weigel_2-34_CHIP-214-A_Rep1_ATH1 GSM133943: Weigel_2-35_CHIP-214-B_Rep2_ATH1 GSM133944: Weigel_2-36_CHIP-214_D_Rep3_ATH1 121: GSE5745 record: Mutant array [Arabidopsis thaliana] Summary: This data was annotated by TAIR (http://arabidopsis.org). Two week-old Arabidopsis aerial tissues from Columbia-0 and cpr5, cpr5npr1, cpr5scv1, cpr5npr1svi1, and npr1 lines were collected for analysis. Experimenter name = Jinyoung Yang Experimenter phone = 919-613-8176, 919-61 Experimenter fax = 919-613-8177 Experimenter department = DCMB GROUP Experimenter institute = Duke University Experimenter address = B361 LSRC Bldg. Experimenter address = Research Dr. Experimenter address = Durham Experimenter zip/postal_code = NC 27708 Experimenter country = USA Samples: 12 GSM133896: Yang_1-1_WT(COL)-1_Rep1_ATH1 GSM133897: Yang_1-2_WT(COL)-2_Rep2_ATH1 GSM133898: Yang_1-3_CPR5-1_Rep1_ATH1 GSM133899: Yang_1-4_CPR5-2_Rep2_ATH1 GSM133900: Yang_1-5_NPR1-1_Rep1_ATH1 GSM133901: Yang_1-6_NPR1-2_Rep2_ATH1 GSM133902: Yang_1-7_CPR5NPR1-1_Rep1_ATH1 GSM133903: Yang_1-8_CPR5NPR1-2_Rep2_ATH1 GSM133904: Yang_1-9_CPR5SCV1-1_Rep1_ATH1 GSM133905: Yang_1-10_CPR5SCV1-2_Rep2_ATH1 GSM133906: Yang_1-11_CPR5NPR1SVI1-1_Rep1_ATH1 GSM133907: Yang_1-12_CPR5NPR1SVI1-2_Rep2_ATH1 122: GSE5729 record: Role of COV in vascular patterning [Arabidopsis thaliana] Summary: The molecular mechanisms that control the ordered patterning of vascular tissue development in plant are not well understood. Several models propose a two component for plant vascular differentiation in which requires both an inducer of vascular tissue an also an inhibitory component that prevents the formation of vascular bundles near pre-existing bundles by a process often termed lateral inhibition. We have identified two recessive allelic mutants in Arabidopsis, designated continuous vascular (cov-1, cov-2), which display a dramatic increase in vascular tissue in the stem in place of the interfascicular region that normally separates the vascular bundles. The mutant plants exhibited normal vascular patterning in leaves and cotyledons. Analysis of the interaction of cov with known auxin signalling mutant and direct analysis of auxin concentrations suggests that cov affects vascular pattering by some mechanism that is independent of auxin. Samples: 8 GSM133747: Turner_A-1-Turne-Mut-Top1_SLD GSM133748: Turner_A-2-Turne-Mut-Top2_SLD GSM133749: Turner_A-3-Turne-Mut-Base1_SLD GSM133750: Turner_A-4-Turne-Mut-Base2_SLD GSM133751: Turner_A-5-Turne-WT-Top1_SLD GSM133752: Turner_A-6-Turne-WT-Top2_SLD GSM133753: Turner_A-7-Turne-WT-Base1_SLD GSM133754: Turner_A-8-Turne-WT-Base2_SLD 123: GSE5748 record: In vitro tracheary element transdifferentiation of Col-0 suspension cells. [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org). Col-0 suspension cells provided by Dr. C. Koncz and Dr. M. Umeda. 15 ml of Arabidopsis Col-0 suspension cells (Mathur et al. 1998) was transferred to 35 ml of a fresh modified Murashige and Skoog (MS) medium supplemented with 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose every 7 day, and cultured on a rotary shaker at 120 rpm in the dark at 22 C for subculture. For xylem vessel element induction, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3, and cultured as described above. The frequency of xylem vessel element formation was calculated as the proportion of xylem vessel elements to the number of living cells and the vessel elements. Samples: 12 GSM133956: Fukuda_1-1_0A_Rep1_ATH1 GSM133957: Fukuda_1-2_0B_Rep2_ATH1 GSM133958: Fukuda_1-3_2A_Rep1_ATH1 GSM133959: Fukuda_1-4_2B_Rep2_ATH1 GSM133960: Fukuda_1-5_4A_Rep1_ATH1 GSM133961: Fukuda_1-6_4B_Rep2_ATH1 GSM133962: Fukuda_1-7_6A_Rep1_ATH1 GSM133963: Fukuda_1-8_6B_Rep2_ATH1 GSM133964: Fukuda_1-9_8A_Rep1_ATH1 GSM133965: Fukuda_1-10_8B_Rep2_ATH1 GSM133966: Fukuda_1-11_10A_Rep1_ATH1 GSM133967: Fukuda_1-12_10B_Rep2_ATH1 124: GSE6147 record: The role of Cdpk6 in development [Arabidopsis thaliana] Summary: The research programme is focussed on determining the role of CDPKs in abiotic stress response. We chose several CDPKs for investigation, some which have been implicated in the response to abiotic stress (Sheen 1996), others whose function is unknown. We constructed gene fusions with YFP as a 3_in-frame fusion to investigate cellular/tissue expression; the gene-specific DNA includes 1.5kb 5'-untranslated region. Plants carrying the Cdpk6-yfp construct show a marked alteration in phenotype: the (probable)-heterozygote is small and bushy and the (probable)-homozygote shows an excess of flower primordia and insufficient leaf development. These plants do not survive. The expression of Cdpk6 as measured using a GUS-promoter fusion is confined to the developing flowerheads although the Cdpk6-YFP plants show despread expression. Samples: 6 GSM142585: JB001_ATH1_A1-1-Boyce-Kan-1 GSM142586: JB001_ATH1_A1-2-Boyce-Kan-2 GSM142587: JB001_ATH1_A2-1-Boyce-cdpk6-yfp-4-1 GSM142588: JB001_ATH1_A2-2-Boyce-cdpk6-yfp-4-2 GSM142589: JB001_ATH1_A3-1-Boyce-Kan-3 GSM142590: JB001_ATH1_A3-2-Boyce-cdpk-yfp-1 125: GSE5731 record: UV-B Responses in Light Grown Plants: Similarities to Biotic Stress [Arabidopsis thaliana] Summary: UV-B (280-320 nm) exposure causes serious damage in plants, limiting their growth and survival, effects that are partly counteracted by repair mechanisms active in plants receiving accompanying visible radiation. Though no particular UV-B receptor has been identified to date, there is strong evidence to indicate that certain aspects of UV-B perception are receptor-mediated. Investigations of down-stream signalling events have thus far indicated broad similarities to pathogen-induced defence responses in plants. In order to identify genes in Arabidopsis that may be up- or down- regulated specifically in response to UV-B exposure and compare them to genes whose expression is altered in plants challenged by an avirulent isolate of Peronospora parasitica (downy mildew), we propose to analyse the transcriptional profiles for the following treatments: 1. Samples: 6 GSM133782: Brueggemann_A-6-Brueg-Pps_SLD GSM133783: Brueggemann_A-1-Brueg-uvb_SLD GSM133784: Brueggemann_A-2-Brueg-uva_SLD GSM133785: Brueggemann_A-3-Brueg-vis_SLD GSM133786: Brueggemann_A-4-Brueg-PpH_SLD GSM133787: Brueggemann_A-5-Brueg-Mck_SLD 126: GSE5730 record: Transcriptional profiling of laser-capture micro-dissected embryonic tissues [Arabidopsis thaliana] Summary: The aim of this BBSRC-funded project is to develop laser-capture microdissection (LCMD) to isolate small cell clusters in different regions of arabidopsis embryos at different stages of development; to develop RNA amplification procedures on dissected tissue sampes; and to use DNA microarray techniques to investigate global transcriptional differences between samples. Cryosectioned embryos of ecotype Col-O of globular, heart and torpedo stage were used to isolate cell clusters from the apical and basal regions, for RNA isolation and amplification. !Samples will be provided as T7-primed cDNA, with three biological replicates for each tissue to be analysed. Each replicate comprises cDNA from pooled tissue samples from ca. 15 embryos. The experimental details have been discussed with Sean May et al. Samples: 27 GSM133755: Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1 GSM133756: Lindsey_1-10_heart-stage-root_Rep1_ATH1 GSM133757: Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1 GSM133758: Lindsey_1-11_heart-stage-root_Rep2_ATH1 GSM133759: Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSM133760: Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSM133761: Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1 GSM133762: Lindsey_1-14_torpedo-root_Rep1_ATH1 GSM133763: Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1 GSM133764: Lindsey_1-16_torpedo-root_Rep2_ATH1 GSM133765: Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1 GSM133766: Lindsey_1-18_torpedo-root_Rep3_ATH1 GSM133767: Lindsey_1-19_torpedo-basal_Rep4_ATH1 GSM133768: Lindsey_1-20_torpedo-basal_Rep5_ATH1 GSM133769: Lindsey_1-21_torpedo-basal_Rep6_ATH1 GSM133770: Lindsey_1-22_torpedo-apical_Rep4_ATH1 GSM133771: Lindsey_1-23_torpedo-apical_Rep5_ATH1 GSM133772: Lindsey_1-24_torpedo-apical_Rep6_ATH1 GSM133773: Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSM133774: Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSM133775: Lindsey_1-27_torpedo-meristem_Rep3_ATH1 GSM133776: Lindsey_1-1_globular-apical_Rep1_ATH1 GSM133777: Lindsey_1-4_globular-basal_Rep1_ATH1 GSM133778: Lindsey_1-2_globular-apical_Rep2_ATH1 GSM133779: Lindsey_1-5_globular-basal_Rep2_ATH1 GSM133780: Lindsey_1-3_globular-apical_Rep3_ATH1 GSM133781: Lindsey_1-6_globular-basal_Rep3_ATH1 127: GSE5632 record: AtGenExpress: Developmental series (flowers and pollen) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 66 GSM131576: ATGE_31_A2 GSM131577: ATGE_31_B2 GSM131578: ATGE_31_C2 GSM131579: ATGE_32_A2 GSM131580: ATGE_32_B2 GSM131581: ATGE_32_C2 GSM131582: ATGE_33_A GSM131583: ATGE_33_B GSM131584: ATGE_33_C GSM131585: ATGE_34_A GSM131586: ATGE_34_B GSM131587: ATGE_34_C GSM131588: ATGE_35_A GSM131589: ATGE_35_B GSM131590: ATGE_35_C GSM131591: ATGE_36_A GSM131592: ATGE_36_B GSM131593: ATGE_36_C GSM131594: ATGE_37_A GSM131595: ATGE_37_B GSM131596: ATGE_37_C GSM131597: ATGE_39_A GSM131598: ATGE_39_B GSM131599: ATGE_39_C GSM131600: ATGE_40_A GSM131601: ATGE_40_B GSM131602: ATGE_40_C GSM131603: ATGE_41_A GSM131604: ATGE_41_B GSM131605: ATGE_41_C GSM131606: ATGE_42_B GSM131607: ATGE_42_C GSM131608: ATGE_42_D GSM131609: ATGE_43_A GSM131610: ATGE_43_B GSM131611: ATGE_43_C GSM131612: ATGE_45_A GSM131613: ATGE_45_B GSM131614: ATGE_45_C GSM131615: ATGE_53_A GSM131616: ATGE_53_B GSM131617: ATGE_53_C GSM131618: ATGE_54_A GSM131619: ATGE_54_B GSM131620: ATGE_54_C GSM131621: ATGE_55_A GSM131622: ATGE_55_B GSM131623: ATGE_55_C GSM131624: ATGE_56_A GSM131625: ATGE_56_B GSM131626: ATGE_56_C GSM131627: ATGE_57_A GSM131628: ATGE_57_B GSM131629: ATGE_57_C GSM131630: ATGE_58_A GSM131631: ATGE_58_B GSM131632: ATGE_58_C GSM131633: ATGE_59_A GSM131634: ATGE_59_B GSM131635: ATGE_59_C GSM131636: ATGE_73_A GSM131637: ATGE_73_B GSM131638: ATGE_73_C GSM131639: ATGE_92_A GSM131640: ATGE_92_B GSM131641: ATGE_92_C 128: GSE5631 record: AtGenExpress: Developmental series (roots) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 21 GSM131555: ATGE_3_A GSM131556: ATGE_3_B GSM131557: ATGE_3_C GSM131558: ATGE_9_A GSM131559: ATGE_9_B GSM131560: ATGE_9_C GSM131561: ATGE_93_A GSM131562: ATGE_93_B GSM131563: ATGE_93_C GSM131564: ATGE_94_A GSM131565: ATGE_94_B GSM131566: ATGE_94_C GSM131567: ATGE_95_A GSM131568: ATGE_95_B GSM131569: ATGE_95_C GSM131570: ATGE_98_A GSM131571: ATGE_98_B GSM131572: ATGE_98_C GSM131573: ATGE_99_A GSM131574: ATGE_99_B GSM131575: ATGE_99_C 129: GSE5630 record: AtGenExpress: Developmental series (leaves) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 60 GSM131495: ATGE_1_A GSM131496: ATGE_1_B GSM131497: ATGE_1_C GSM131498: ATGE_5_A GSM131499: ATGE_5_B GSM131500: ATGE_5_C GSM131501: ATGE_10_A GSM131502: ATGE_10_B GSM131503: ATGE_10_C GSM131504: ATGE_11_A GSM131505: ATGE_11_B GSM131506: ATGE_11_C GSM131507: ATGE_12_A GSM131508: ATGE_12_B GSM131509: ATGE_12_C GSM131510: ATGE_13_A GSM131511: ATGE_13_B GSM131512: ATGE_13_C GSM131513: ATGE_14_A GSM131514: ATGE_14_B GSM131515: ATGE_14_C GSM131516: ATGE_15_A GSM131517: ATGE_15_B GSM131518: ATGE_15_C GSM131519: ATGE_16_A GSM131520: ATGE_16_B GSM131521: ATGE_16_C GSM131522: ATGE_17_A GSM131523: ATGE_17_B GSM131524: ATGE_17_C GSM131525: ATGE_18_A GSM131526: ATGE_18_B GSM131527: ATGE_18_C GSM131528: ATGE_19_A GSM131529: ATGE_19_B GSM131530: ATGE_19_C GSM131531: ATGE_20_A GSM131532: ATGE_20_B GSM131533: ATGE_20_C GSM131534: ATGE_21_A GSM131535: ATGE_21_B GSM131536: ATGE_21_C GSM131537: ATGE_25_A GSM131538: ATGE_25_B GSM131539: ATGE_25_C GSM131540: ATGE_26_A GSM131541: ATGE_26_B GSM131542: ATGE_26_C GSM131543: ATGE_87_A GSM131544: ATGE_87_B GSM131545: ATGE_87_C GSM131546: ATGE_89_A GSM131547: ATGE_89_B GSM131548: ATGE_89_C GSM131549: ATGE_90_A GSM131550: ATGE_90_B GSM131551: ATGE_90_D GSM131552: ATGE_91_A GSM131553: ATGE_91_B GSM131554: ATGE_91_C 130: GSE5629 record: AtGenExpress: Developmental series (seedlings and whole plants) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 24 GSM131471: ATGE_7_A2 GSM131472: ATGE_7_B2 GSM131473: ATGE_7_C2 GSM131474: ATGE_22_A GSM131475: ATGE_22_B GSM131476: ATGE_22_C GSM131477: ATGE_23_A GSM131478: ATGE_23_B GSM131479: ATGE_23_C GSM131480: ATGE_24_A GSM131481: ATGE_24_B GSM131482: ATGE_24_C GSM131483: ATGE_96_A GSM131484: ATGE_96_B GSM131485: ATGE_96_C GSM131486: ATGE_97_A GSM131487: ATGE_97_B GSM131488: ATGE_97_C GSM131489: ATGE_100_A GSM131490: ATGE_100_B GSM131491: ATGE_100_C GSM131492: ATGE_101_A GSM131493: ATGE_101_B GSM131494: ATGE_101_C 131: GSE5628 record: AtGenExpress: Stress Treatments (Heat stress) [Arabidopsis thaliana] Summary: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. Samples: 32 GSM131439: AtGen_6-9711_Heatstress-Shoots-0.25h_Rep1 GSM131440: AtGen_6-9712_Heatstress-Shoots-0.25h_Rep2 GSM131441: AtGen_6-9721_Heatstress-Roots-0.25h_Rep1 GSM131442: AtGen_6-9722_Heatstress-Roots-0.25h_Rep2 GSM131443: AtGen_6-9111_Heatstress-Shoots-0.5h_Rep1 GSM131444: AtGen_6-9112_Heatstress-Shoots-0.5h_Rep2 GSM131445: AtGen_6-9121_Heatstress-Roots-0.5h_Rep1 GSM131446: AtGen_6-9122_Heatstress-Roots-0.5h_Rep2 GSM131447: AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1 GSM131448: AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2 GSM131449: AtGen_6-9221_Heatstress-Roots-1.0h_Rep1 GSM131450: AtGen_6-9222_Heatstress-Roots-1.0h_Rep2 GSM131451: AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1 GSM131452: AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2 GSM131453: AtGen_6-9321_Heatstress-Roots-3.0h_Rep1 GSM131454: AtGen_6-9322_Heatstress-Roots-3.0h_Rep2 GSM131455: AtGen_6-9811_Heatstress(3h)+1hrecovery-Shoots-4.0h_Rep1 GSM131456: AtGen_6-9812_Heatstress(3h)+1hrecovery-Shoots-4.0h_Rep2 GSM131457: AtGen_6-9821_Heatstress(3h)+1hrecovery-Roots-4.0h_Rep1 GSM131458: AtGen_6-9822_Heatstress(3h)+1hrecovery-Roots-4.0h_Rep2 GSM131459: AtGen_6-9411_Heatstress(3h)+3hrecovery-Shoots-6.0h_Rep1 GSM131460: AtGen_6-9412_Heatstress(3h)+3hrecovery-Shoots-6.0h_Rep2 GSM131461: AtGen_6-9421_Heatstress(3h)+3hrecovery-Roots-6.0h_Rep1 GSM131462: AtGen_6-9422_Heatstress(3h)+3hrecovery-Roots-6.0h_Rep2 GSM131463: AtGen_6-9511_Heatstress(3h)+9hrecovery-Shoots-12.0h_Rep1 GSM131464: AtGen_6-9512_Heatstress(3h)+9hrecovery-Shoots-12.0h_Rep2 GSM131465: AtGen_6-9521_Heatstress(3h)+9hrecovery-Roots-12.0h_Rep1 GSM131466: AtGen_6-9522_Heatstress(3h)+9hrecovery-Roots-12.0h_Rep2 GSM131467: AtGen_6-9611_Heatstress(3h)+21hrecovery-Shoots-24.0h_Rep1 GSM131468: AtGen_6-9612_Heatstress(3h)+21hrecovery-Shoots-24.0h_Rep2 GSM131469: AtGen_6-9621_Heatstress(3h)+21hrecovery-Roots-24.0h_Rep1 GSM131470: AtGen_6-9622_Heatstress(3h)+21hrecovery-Roots-24.0h_Rep2 132: GSE4847 record: Expression data from tocopherol deficient seedlings of Arabidopsis [Arabidopsis thaliana] Summary: Tocopherols (Vitamin E) are lipophilic antioxidants that are synthesized by all plants and are particularly abundant in seeds. Two tocopherol deficient mutant loci were used to examine how tocopherol deficiency impacts global gene expression during the critical peroid of germination and early seedling development when tocopherols are essential. vte1 lacks all tocopherols, but accumulates the tocopherol pathway intermediate DMPBQ,. vte2 which lacks all tocopherols and pathway intermediates. We used microarrays to examine the global gene expression in early seedlings and identify distinct classes of genes whose expression is affected by tocopherol deficient mutants vte1 and vte2. Samples: 18 GSM109107: wild-type(Col-0) 1 day, biological rep1 GSM109108: wild-type(Col-0) 1 day, biological rep2 GSM109109: wild-type(Col-0) 1 day, biological rep3 GSM109110: vte1-1(Col-0) 1 day, biological rep1 GSM109111: vte1-1(Col-0) 1 day, biological rep2 GSM109112: vte1-1(Col-0) 1 day, biological rep3 GSM109113: vte2-1(Col-0) 1 day, biological rep1 GSM109114: vte2-1(Col-0) 1 day, biological rep2 GSM109115: vte2-1(Col-0) 1 day, biological rep3 GSM109116: wild-type(Col-0) 3 day, biological rep1 GSM109117: wild-type(Col-0) 3 day, biological rep2 GSM109118: wild-type(Col-0) 3 day, biological rep3 GSM109119: vte1-1(Col-0) 3 day, biological rep1 GSM109120: vte1-1(Col-0) 3 day, biological rep2 GSM109121: vte1-1(Col-0) 3 day, biological rep3 GSM109122: vte2-1(Col-0) 3 day, biological rep1 GSM109123: vte2-1(Col-0) 3 day, biological rep2 GSM109124: vte2-1(Col-0) 3 day, biological rep3 133: GSE4455 record: Gene expression in roots of slim1 and the parental line grown +/-S condition [Arabidopsis thaliana] Summary: Plants utilize soil sulfate for production of sulfur-containing amino acids that serve as essential dietary sulfur sources for animals. Despite the global nutritional significance of this fundamental metabolic process in nature, transcription factors regulating the plant sulfur assimilation pathways have never been discovered. We isolated sulfur limitation1 (slim1) mutants from Arabidopsis, showing abnormally low expression of SULTR1;2 sulfate transporter, by screening responsiveness of SULTR1;2 promoter-GFP, as an indicator, to sulfur limitation. SLIM1 encoded an EIL-family transcription factor, EIL3. To clarify the siganificance of SLIM1 function in sulfur responsive gene expression, we analyzed the transcriptome profiles in slim1-1, slim1-2 and the parental line under +S and -S conditi. Samples: 12 GSM100170: P-S1500, biological rep1 GSM100171: P-S1500, biological rep2 GSM100172: P-S15, biological rep1 GSM100173: P-S15, biological rep2 GSM100174: slim1-1-S1500, biological rep1 GSM100175: slim1-1-S1500, biological rep2 GSM100176: slim1-1-S15, biological rep1 GSM100177: slim1-1-S15, biological rep2 GSM100178: slim1-2-S1500, biological rep1 GSM100179: slim1-2-S1500, biological rep2 GSM100180: slim1-2-S15, biological rep1 GSM100181: slim1-2-S15, biological rep2 134: GSE6556 record: Expression profiling of A. thaliana wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2) [Arabidopsis thaliana] Summary: To reveal the underlying molecular mechanism of GH3.5 action in modulating the SA and auxin pathways, we performed transcriptional profiling of gh3.5-1D plants after infection with or without Pst DC3000(avrRpt2) on a global scale using the Affymetrix Arabidopsis ATH1 GeneChip Samples: 12 GSM151694: Col-0 uninoculated, biological replicate 1 GSM151695: Col-0 uninoculated, biological replicate 2 GSM151696: Col-0 uninoculated, biological replicate 3 GSM151697: gh3.5-1D uninoculated, biological replicate 1 GSM151698: gh3.5-1D uninoculated, biological replicate 2 GSM151699: gh3.5-1D uninoculated, biological replicate 3 GSM151700: Col-0 48 hpi, biological replicate 1 GSM151701: Col-0 48 hpi, biological replicate 2 GSM151702: Col-0 48 hpi, biological replicate 3 GSM151703: gh3.5-1D 48 hpi, biological replicate 1 GSM151704: gh3.5-1D 48 hpi, biological replicate 2 GSM151705: gh3.5-1D 48 hpi, biological replicate 3 135: GSE6516 record: Silverleaf whitefly 2nd instar feeding on 7-week old Arabidopsis thaliana rosette leaves [Arabidopsis thaliana] Summary: Phloem-feeding pests cause extensive crop damage throughout the world yet little is understood about how plants perceive and defend themselves from these threats. The silverleaf whitefly (SLWF; Bemisia tabaci type B) is a good model for studying phloem-feeding insect-plant interactions as SLWF nymphs cause little wounding and have a long, continuous interaction with the plant. Using the Arabidopsis ATH1 GeneChip, the global responses to Silverleaf Whitefly 2nd instar feeding were examined. Samples: 4 GSM149814: SLWF uninfested arabidopsis rosette tissue, replicate 1 GSM149815: SLWF uninfested arabidopsis rosette tissue, replicate 2 GSM149816: SLWF infested arabidopsis rosette tissue, replicate 1 GSM149817: SLWF infested arabidopsis rosette tissue, replicate 2 136: GSE6203 record: Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1 [Arabidopsis thaliana] Summary: Background: Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomics strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis (BSA) and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil. Methodology/Principal Findings: Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that Ts-1 and Tsu-1 accumulate higher shoot levels of Na+ than Col-0 and other accessions. Samples: 13 GSM143298: Low_Na_seg_pool_ts_col_F2 GSM143299: High_Na_seg_pool_ts_col_F2 GSM143300: Ts_genomic_hyb_3 GSM143301: Ts_genomic_hyb_2 GSM143302: Ts_genomic_hyb_1 GSM143303: col3DNA GSM143304: col1DNA GSM143305: col2DNA GSM143306: High_Na_seg_pool_tsu_col_F2 GSM143307: Low_Na_seg_pool_tsu_col_F2 GSM143308: Tsu_genomic_hyb_3 GSM143309: Tsu_genomic_hyb_2 GSM143310: Tsu_genomic_hyb_1 137: GSE4760 record: Heat shock response of HsfA2 knockout plants [Arabidopsis thaliana] Summary: The expression of heat-shock proteins (Hsps) induced by a non-lethal heat treatment confers acquired thermotolerance (AT) to organisms against a subsequent challenge of otherwise lethal temperature. After stress signal lifted, AT gradually decayed with the decline of Hsps during recovery period. The duration of AT may be critical for sessile organisms, such as plants, to survive repeated heat stress in the environment. To identify heat-induced genes involved in duration of AT, we took a reverse-genetics approach by screening for Arabidopsis T-DNA insertion mutants that show decreased thermotolerance after a long recovery at non-stress condition following a conditioning treatment. Among the tested mutants corresponding to 47 genes, only the HsfA2 knockout mutant showed significant phenotype. Samples: 12 GSM107436: Wt_seedling_control_rep1 GSM107443: Wt_seedling_control_rep2 GSM107444: HsfA2KO_seedling_control_rep1 GSM107445: HsfA2KO_seedling_control_rep2 GSM107446: Wt_seedling_HS37_rep1 GSM107577: Wt_seedling_HS37_rep2 GSM107579: HsfA2KO_seedling_HS37_rep1 GSM107580: HsfA2KO_seedling_HS37_rep2 GSM107586: Wt_seedling_HS44_rep1 GSM107587: Wt_seedling_HS44_rep2 GSM107589: HsfA2KO_seedling_HS44_rep1 GSM107591: HsfA2KO_seedling_HS44_rep2 138: GSE5896 record: Overexpression of TELOMERASE ACTIVATOR 1 (TAC1) [Arabidopsis thaliana] Summary: The goal of this investigation was to identify putative targets of the TELOMERASE ACTIVATOR 1 transcription factor. Samples: 6 GSM137118: wild type (Columbia) leaf replicate 1 GSM137119: wild type (Columbia) leaf replicate 2 GSM137120: wild type (Columbia) leaf replicate 3 GSM137121: tac1-1D leaf replicate 1 GSM137122: tac1-1D leaf replicate 2 GSM137123: tac1-1D leaf replicate 3 139: GSE5770 record: col0,gun1,abi4-102, w/wo lincomycin [Arabidopsis thaliana] Summary: To test the relationship between GUN1 and ABI4 Samples: 12 GSM134767: abi4-102_5day_-lincomycin_rep1 GSM134768: abi4-102_5day_-lincomycin_rep2 GSM134769: abi4-102_5day_+lincomycin_rep1 GSM134771: abi4-102_5day_+lincomycin_rep2 GSM134772: Col-0_5day_-lincomycin_rep1 GSM134774: Col-0_5day_-lincomycin_rep2 GSM134775: Col-0_5day_+lincomycin_rep1 GSM134777: Col-0_5day_+lincomycin_rep2 GSM134779: gun1-1_5day_-lincomycin_rep1 GSM134780: gun1-1_5day_-lincomycin_rep2 GSM134782: gun1-1_5day_+lincomycin_rep1 GSM134783: gun1-1_5day_+lincomycin_rep2 140: GSE5759 record: red illumination w/o lincomycin [Arabidopsis thaliana] Summary: To identify putative regulatory elements enriched in the promoters of target genes of the PGE-dependent retrograde signaling pathway, we analyzed 500 bp regions of sequence upstream of genes whose expression was down-regulated by lincomycin. We treated dark-grown Arabidopsis seedlings with lincomycin, sampled them before or after a short illumination and examined the genomic response using Affymetrix ATH1 oligonucleotide microarrays. Differentially regulated genes were ranked based on descending degree of significance (p-value) and the top 50 genes affected by lincomycin in dark grown seedlings and top 50 genes affected by the antibiotic after illumination were selected for further analysis. Samples: 8 GSM134513: Col-0_4day_dark_-lincomycin_rep1 GSM134514: Col-0_4day_dark_-lincomycin_rep2 GSM134515: Col-0_4day_dark_+lincomycin_rep1 GSM134516: Col-0_4day_dark_+lincomycin_rep2 GSM134517: Col-0_4day_red illumination_-lincomycin_rep1 GSM134518: Col-0_4day_red illumination_-lincomycin_rep2 GSM134519: Col-0_4day_red illumination_+lincomycin_rep1 GSM134520: Col-0_4day_red illumination _+lincomycin_rep2 141: GSE5523 record: Environmental Genomics of Calcicole-calcifuge physiology [Arabidopsis thaliana] Summary: The purpose of this set of arrays is to provide a third replicate to use in data analysis addition to the 2 previous replicates for all samples already generated on this project. Our hypothesis is that adaptation to a calcareous environment will be reflected in altered gene expression including genes encoding transporters, ion channels, transcription factors, etc. To test this hypothesis we grew a laboratory non-calcicole (Col-4) and a laboratory calcicole (Cal-0) ecotypes of A. thaliana at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compare the patterns of gene expression by microarray analysis. We then collected from the wild, a putative calcicole ecotype (Elland)and a putative non-calcicole (Penicuik) and grew both at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compared expression profiles to the laboratory ecotypes. Samples: 8 GSM128704: Shirras_3-1_LabCalcicole-1mM-CaCl2_Rep1_ATH1 GSM128705: Shirras_3-2_LabCalcifuge-1mM-CaCl2_Rep1_ATH1 GSM128706: Shirras_3-3_LabCalcicole-12.5mM-CaCl2_Rep1_ATH1 GSM128707: Shirras_3-4_LabCalcifuge-12.5mM-CaCl2_Rep1_ATH1 GSM128708: Shirras_3-5_WildEcotype-low-soil-pH-1mM-CaCl2_Rep1_ATH1 GSM128709: Shirras_3-6_WildEcotype-high-soil-pH-1mM-CaCl2_Rep1_ATH1 GSM128710: Shirras_3-7_WildEcotype-low-soil-pH-12.5mM-CaCl2_Rep1_ATH1 GSM128711: Shirras_3-8_WildEcotype-high-soil-pH-12.5mM-CaCl2_Rep1_ATH1 142: GSE5522 record: Low chronic exposure of Arabidopsis thaliana to Caesium-137 [Arabidopsis thaliana] Summary: Arabidopsis thaliana plants are grown for one week in a hydroponic growth system and transferred to new plant medium containing low levels of Caesium-137 (control is transferred to new medium with no radioactivity) and left for further two weeks. Levels of Caesium-137 are chosen according to research and are reflecting occurring levels found in radioactive contaminated soil. The plants are then harvested and the samples divided into shoot and root samples. Experimenter name = Yu-Jin Heinekamp Experimenter phone = 0044-117-3442102 Experimenter address = University of the West of England (UWE) Experimenter address = Faculty of Applied Sciences Experimenter address = Center for Research in Plants, GRI Experimenter address = Coldharbour Lane Experimenter address = Bristol Experimenter zip/po. Samples: 12 GSM128692: Heinekamp_1-1_control-shoot_Rep1_ATH1 GSM128693: Heinekamp_1-2_control-root_Rep1_ATH1 GSM128694: Heinekamp_1-3_cs-shoot_Rep1_ATH1 GSM128695: Heinekamp_1-4_cs-root_Rep1_ATH1 GSM128696: Heinekamp_1-5_control-shoot_Rep2_ATH1 GSM128697: Heinekamp_1-6_control-root_Rep2_ATH1 GSM128698: Heinekamp_1-7_cs-shoot_Rep2_ATH1 GSM128699: Heinekamp_1-8_cs-root_Rep2_ATH1 GSM128700: Heinekamp_1-9_control-shoot_Rep3_ATH1 GSM128701: Heinekamp_1-10_control-root_Rep3_ATH1 GSM128702: Heinekamp_1-11_cs-shoot_Rep3_ATH1 GSM128703: Heinekamp_1-12_cs-root_Rep3_ATH1 143: GSE5521 record: Comparative ABA-treatment of Col-O vector control and transgenic plants [Arabidopsis thaliana] Summary: The aim of this experiment is to understand the impact of overexpression of ERD15 on the transcriptome of Arabidopsis thaliana. ERD15 was isolated from a screen for genes rapidly induced after pathogen treatment from Arabidopsis. This gene was originally found as early responsive to drought (Kiyosue et al., 1994, Plant Physiol 106, 1707). ABA is central phytohormone in drought response, but increasing information is pointing to its significant role in pathogen responses as well. We are interested to see the effect of this hormone on plants overexpressing ERD15 compared to control plants. The samples (rosette leaves)will be harvested from 3-week old soil grown plants 90 min after spraying with 100 micromolar ABA. Comparison will be made with non-treated plant samples. Experimenter name = E. Samples: 4 GSM128688: Helenius_1-1_control-non-treated_Rep1_ATH1 GSM128689: Helenius_1-2_control-ABA-treated_Rep1_ATH1 GSM128690: Helenius_1-3_ERD15-oex-non-treated_Rep1_ATH1 GSM128691: Helenius_1-4_ERD15 oex-ABA-treated_Rep1_ATH1 144: GSE5520 record: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction [Arabidopsis thaliana] Summary: Pseudomonas syringae pv. tomato DC3000 (Pst) is a virulent pathogen, which causes disease on tomato and Arabidopsis. The type III secretion system (TTSS) plays a key role in pathogenesis by translocating virulence effectors from the bacteria into the plant host cell, while the phytotoxin coronatine (COR) contributes to virulence and disease symptom development. Recent studies suggest that both the TTSS and and COR are involved in the suppression of host basal defenses. However, little is known about the interplay between the host gene expression associated with basal defenses and the virulence activities of the TTSS and COR during infection. The global effects of the TTSS and COR on host gene expression associated with other host cellular processes during bacterial infection are also not well characterized. Samples: 40 GSM128648: Underwood_1-1_Cor-10e6-24h_Rep1_ATH1 GSM128649: Underwood_1-2_Cor-10e6-24h_Rep2_ATH1 GSM128650: Underwood_1-3_Cor-10e6-24h_Rep3_ATH1 GSM128651: Underwood_1-4_Cor-hrpS-10e6-24h_Rep1_ATH1 GSM128652: Underwood_1-5_Cor-hrpS-10e6-24h_Rep2_ATH1 GSM128653: Underwood_1-6_Cor-hrpS-10e6-24h_Rep3_ATH1 GSM128654: Underwood_1-7_DC3000-10e6-24h_Rep1_ATH1 GSM128655: Underwood_1-8_DC3000-10e6-24h_Rep2_ATH1 GSM128656: Underwood_1-9_DC3000-10e6-24h_Rep3_ATH1 GSM128657: Underwood_1-10_Mock-Inoculum-24h_Rep1_ATH1 GSM128658: Underwood_1-11_Mock-Inoculum-24h_Rep2_ATH1 GSM128659: Underwood_1-12_Mock-Inoculum-24h_Rep3_ATH1 GSM128660: Underwood_1-13_Cor-5x10e7-10h_Rep1_ATH1 GSM128661: Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1 GSM128662: Underwood_1-15_Cor-5x10e7-10h_Rep3_ATH1 GSM128663: Underwood_1-16_Cor-hrpS-5x10e7-10h_Rep1_ATH1 GSM128664: Underwood_1-18_Cor-hrpS-5x10e7-10h_Rep3_ATH1 GSM128665: Underwood_1-17_Cor-hrpS-5x10e7-10h_Rep2_ATH1 GSM128666: Underwood_1-19_Mock-Inoculum-10h_Rep1_ATH1 GSM128667: Underwood_1-20_Mock-Inoculum-10h_Rep2_ATH1 GSM128668: Underwood_1-21_Mock-Inoculum-10h_Rep3_ATH1 GSM128669: Underwood_1-22_hrpAfliC-10e8-7h_Rep1_ATH1 GSM128670: Underwood_1-23_hrpAfliC-10e8-7h_Rep2_ATH1 GSM128671: Underwood_1-24_hrpAfliC-10e8-7h_Rep3_ATH1 GSM128672: Underwood_1-27_hrpA-10e8-7h_Rep3_ATH1 GSM128673: Underwood_1-25_hrpA-10e8-7h_Rep1_ATH1 GSM128674: Underwood_1-26_hrpA-10e8-7h_Rep2_ATH1 GSM128675: Underwood_1-28_DC3000-10e8-7h_Rep1_ATH1 GSM128676: Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1 GSM128677: Underwood_1-30_DC3000-10e8-7h_Rep3_ATH1 GSM128678: Underwood_1-31_Mock-Inoculum-7h_Rep1_ATH1 GSM128679: Underwood_1-32_Mock-Inoculum-7h_Rep2_ATH1 GSM128680: Underwood_1-33_Mock-Inoculum-7h_Rep3_ATH1 GSM128681: Underwood_1-34_Mock-Inoculum-7h_Rep4_ATH1 GSM128682: Underwood_1-35_E.coli-0157-H7-10e8-7h_Rep1_ATH1 GSM128683: Underwood_1-36_E.coli-0157-H7-10e8-7h_Rep2_ATH1 GSM128684: Underwood_1-37_E.coli-0157-H7-10e8-7h_Rep3_ATH1 GSM128685: Underwood_1-38_E.coli-TUV86-2-fliC-10e8-7h_Rep1_ATH1 GSM128686: Underwood_1-39_E.coli-TUV86-2-fliC-10e8-7h_Rep2_ATH1 GSM128687: Underwood_1-40_E.coli-TUV86-2-fliC-10e8-7h_Rep3_ATH1 145: GSE5539 record: Over-expression of MBF1c enhances stress tolerance [Arabidopsis thaliana] Summary: Multiprotein bridging factor 1c MBF1c (At3g24500) is a stress-response transcription co-activator. To test the function of MBF1c, we over-expressed it in transgenic Arabidopsis plants using the 35S-CaMV promoter. T4 seeds form 3 independent lines were tested for their tolerance to biotic and abiotic stress conditions. Constitutive expression of MBF1c in Arabidopsis enhanced the tolerance of transgenic plants to bacterial infection, salinity, heat and osmotic stress. Moreover, the enhanced tolerance of transgenic plants to osmotic and heat stress was maintained even when these two stresses were combined. The expression of MBF1c in transgenic plants augmented the accumulation of a number of sugars and defense transcrtipts in response to heat stress. Transcriptome profiling and inhibitor studies suggest that MBF1c expression enhances the tolerance of transgenic plants to heat and osmotic stress by partially activating, or perturbing, the ethylene-response signal transduction pathway. Samples: 6 GSM128877: Mittler_1-1_control_Rep1_ATH1 GSM128878: Mittler_1-2_control_Rep2_ATH1 GSM128879: Mittler_1-3_control_Rep3_ATH1 GSM128880: Mittler_1-4_MBF1c_Rep1_ATH1 GSM128881: Mittler_1-5_MBF1c_Rep2_ATH1 GSM128882: Mittler_1-6_MBF1c_Rep3_ATH1 146: GSE5537 record: Targets of AtWRKY27 in Arabidopsis leaves [Arabidopsis thaliana] Summary: The Arabidopsis transcription factor WRKY27 was found to be involved in plant defense towards Ralstonia solanacearum GMI1000. To identify target genes of WRKY27, we introduced a functional tagged version of WRKY27 into two independent Arabidopsis wrky27 knockout lines (ecotype Columbia) under the control of the estrogen receptor-based chemical-inducible system. 18 days old plants grown on soil (Metro Mix 200) at 22oC under a 10/14 h light/dark cycle were treated for 6h with 10 microM beta-estradiol after which RNA was immediately isolated. The two independent knockout lines transformed with the empty vectors (pMD::XVE-SALK and pMD::XVE-ETL) served as controls and were grown under the same conditions and treated identically as the experimental plants. Experimenter name = Shahid Mukhtar Experimenter phone = +49-221-5062-310 Experimenter fax = +49-221-5062-353 Experimenter address = Max.Planck-Institute for Plant Breeding Experimenter address = Dept. Samples: 4 GSM128809: Mukhtar_1-1_XVE-SALK_Rep1_ATH1 GSM128810: Mukhtar_1-2_XVE-ETL_Rep1_ATH1 GSM128811: Mukhtar_1-3_WK27-XVE-SALK_Rep1_ATH1 GSM128812: Mukhtar_1-4_WK27-XVE-ETL_Rep1_ATH1 147: GSE5530 record: Hydrogen peroxide stress and Zat12 over-expression in Arabidopsis. [Arabidopsis thaliana] Summary: In this experiment we tested the transcriptome of transgenic Arabidopsis seedlings (5-day-old) constitutively expressing the zinc-finger protein Zat12 (At5g59820) under the control of the 35S-CaMV promoter (Zat12). The transcriptome of these seedlings was compared to that of wild type seedlings grown under the same conditions (WT) and to that of wild type seedlings grown under the same conditions and subjected to a hydrogen peroxide stress (WT+H2O2). Hydrogen peroxide treatment was performed by applying 20 mM hydrogen peroxide for 1 hour. In parallel to these experiments transgenic plants expressing Zat12 were subjected to a similar hydrogen peroxide stress (Zat12+H2O2). All treatments were performed with similar size and age seedlings grown in liquid culture (MS) and sampled at the same time as described by Davletova et al., 2005. Samples: 12 GSM128757: Mittler_2-1_wildtype_Rep1_ATH1 GSM128758: Mittler_2-2_wildtype_Rep2_ATH1 GSM128759: Mittler_2-3_wildtype_Rep3_ATH1 GSM128760: Mittler_2-4_wildtype+H2O2_Rep1_ATH1 GSM128761: Mittler_2-5_wildtype+H2O2_Rep2_ATH1 GSM128762: Mittler_2-6_wildtype+H2O2_Rep3_ATH1 GSM128763: Mittler_2-7_Zat12_Rep1_ATH1 GSM128764: Mittler_2-8_Zat12_Rep2_ATH1 GSM128765: Mittler_2-9_Zat12_Rep3_ATH1 GSM128766: Mittler_2-10_Zat12+H2O2_Rep1_ATH1 GSM128767: Mittler_2-11_Zat12+H2O2_Rep2_ATH1 GSM128768: Mittler_2-12_Zat12+H2O2_Rep3_ATH1 148: GSE5529 record: Arabidopsis E2F target genes [Arabidopsis thaliana] Summary: Entry into the S phase of the cell cycle is controlled by the E2F transcitption factors that induce the transcription of genes required for cell cycle progression and DNA replication. To identify E2F target genes of Arabidopsis on a genome-wide scale, the transcriptome of wild-type plants was compared with that one of plants ectopically expressing the E2Fa-DPa genes. In four independent experiments, E2Fa-DPa overexpressing plants were grown side-to-side with wild type (Col-0) plants. RNA was extracted from 6-day-old seedlings. Each biological sample was harvested and processed independently, and finally all probed individually to Affymetrix ATH1 microarrays, resulting into 8 hybridization signals for each probeset. Experimenter name = Lieven De Veylder Experimenter phone = +32 9 3313961 E. Samples: 8 GSM128749: De Veylder_1-1_wildtype_Rep1_ATH1 GSM128750: De Veylder_1-2_wildtype_Rep2_ATH1 GSM128751: De Veylder_1-3_wildtype_Rep3_ATH1 GSM128752: De Veylder_1-4_wildtype_Rep4_ATH1 GSM128753: De Veylder_1-5_E2Fa-Dpa_Rep1_ATH1 GSM128754: De Veylder_1-6_E2Fa-Dpa_Rep2_ATH1 GSM128755: De Veylder_1-7_E2Fa-Dpa_Rep3_ATH1 GSM128756: De Veylder_1-8_E2Fa-Dpa_Rep4_ATH1 149: GSE5528 record: Identifying targets of FLC at 27oC [Arabidopsis thaliana] Summary: FLOWERING LOCUS C (FLC) is a MADS box transcription factor that plays a well characterised role in repressing the vegetative to floral transition of Arabidopsis thaliana. FLC has also been shown to affect the Arabidopsis circadian clock, with mutant seedlings showing short circadian periods. In a previous study, we identified the temperature-dependent circadian period QTL PerCv5b near the FLC locus on the top arm of Chromosome 5. PerCv5b caused a significant period effect at 27oC but not at 12oC or 22oC. Temperature-dependent circadian period phenotypes and a known polymorphism in the Ler allele made FLC a strong candidate gene for PerCv5b. The period effect of FLC was enhanced by combination with alleles of FRIGIDA (FRI), a gene shown to up-regulate FLC's expression. We were interested in identifying how FLC affects the circadian clock, so we decided to identify its target genes. Samples: 4 GSM128745: Edwards_3-1_FRI-FLC-wt1_Rep1_ATH1 GSM128746: Edwards_3-2_fri-flc1_Rep1_ATH1 GSM128747: Edwards_3-3_FRI-FLC-wt2_Rep2_ATH1 GSM128748: Edwards_3-4_fri-flc2_Rep2_ATH1 150: GSE5535 record: Response to cold, soil grown plants [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in Col-0 plants grown in soil in response to low temperature over time. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Samples: 8 GSM128797: Zarka_2-1_MT-0HCA(SOIL)_Rep1_ATH1 GSM128798: Zarka_2-2_MT-0HCB(SOIL)_Rep2_ATH1 GSM128799: Zarka_2-3_MT-1HCA(SOIL)_Rep1_ATH1 GSM128800: Zarka_2-4_MT-1HCB(SOIL)_Rep2_ATH1 GSM128801: Zarka_2-5_MT-24HCA(SOIL)_Rep1_ATH1 GSM128802: Zarka_2-6_MT-24HCB(SOIL)_Rep2_ATH1 GSM128803: Zarka_2-7_MT-7DCA(SOIL)_Rep1_ATH1 GSM128804: Zarka_2-8_MT-7DCB(SOIL)_Rep2_ATH1 151: GSE5533 record: Tissue Type Arrays of Columbia-0 [Arabidopsis thaliana] Summary: This experiment has been annotated by TAIR (http://arabidopsis.org). In this experiment, different tissue preparations of wild type Columbia-0 Arabidopsis thaliana plants were hybridized and run on the ATH1 Affymetrix platform. Experimenter name = Chris Somerville Experimenter phone = 650-325-1521 ext203 Experimenter fax = 650-325-6857 Experimenter address = Plant Biology Experimenter address = Carnegie Institution Experimenter address = 260 Panama Street Experimenter address = Stanford Experimenter zip/postal_code = CA 94305-1297 Experimenter country = USA Samples: 11 GSM128778: Somerville_1-1_leaf-GC2_Rep1_ATH1 GSM128779: Somerville_1-2_leaf-GH1_Rep1_ATH1 GSM128780: Somerville_1-3_leaf-GH2_Rep2_ATH1 GSM128781: Somerville_1-4_flower-GC5_Rep1_ATH1 GSM128782: Somerville_1-5_flower-GC6_Rep2_ATH1 GSM128783: Somerville_1-6_flower-GH5_Rep1_ATH1 GSM128784: Somerville_1-7_flower-GH6_Rep2_ATH1 GSM128785: Somerville_1-8_stem-GC7_Rep1_ATH1 GSM128786: Somerville_1-9_stem-GC8_Rep2_ATH1 GSM128787: Somerville_1-10_stem-GH7_Rep1_ATH1 GSM128788: Somerville_1-11_stem-GH8_Rep2_ATH1 152: GSE5526 record: Transcriptional Programs of Early Reproductive Stages in Arabidopsis [Arabidopsis thaliana] Summary: The life cycle of flowering plants alternates between a diploid sporophytic and a haploid gametophytic generation. After fertilization of each the egg and central cells by one male gamete, the development of both fertilization products occurs coordinated with the maternally derived seed coat and carpel tissues forming the fruit. The reproduction program is likely to involve the concerted activity of many genes. To identify genes with specific functions during reproduction, we have analyzed the expression profile of an 22,000 genes present on the Arabidopsis ATH1 microarray during three stages of flower and fruit development. We found 1,886 genes regulated during reproductive development and 1,043 genes that were specifically expressed during reproduction. When compared to cells from an Arabidopsis suspension culture, S-phase genes were underrepresented and G2 and M-phase genes were strongly enriched in the set of specific genes, indicating that important functions during reproduction are exerted in the G2 and M phases of the cell cycle. Samples: 6 GSM128729: Hennig_1-1_flower-buds-CK_021114_1_A_Rep1_ATH1 GSM128730: Hennig_1-2_flowers-CK_021114_2_A_Rep1_ATH1 GSM128731: Hennig_1-3_siliques-CK_021114_3_A_Rep1_ATH1 GSM128732: Hennig_1-4_flower-buds-CK_021114_1_B_Rep2_ATH1 GSM128733: Hennig_1-5_flowers-CK_021114_2_B_Rep2_ATH1 GSM128734: Hennig_1-6_siliques-CK_021114_3_B_Rep2_ATH1 153: GSE5524 record: Gene Expression During Recovery from Freezing [Arabidopsis thaliana] Summary: Freezing causes physiological changes even in a hardy, cold-acclimated wild type. During recovery from freezing, gene expression will reflect the induction of damage-repair processes distinct from the damage-prevention associated with cold acclimation. This will be detected by observing the wild-type transcriptome at two time points during recovery from a freezing episode. The appropriate control is the unfrozen, cold-acclimated wild type. Experimenter name = Glenn Thorlby Experimenter phone = 01874 443770 Experimenter address = School of biological Sciences Experimenter address = Bourne Building Experimenter address = Royal Holloway Experimenter address = Egham Experimenter zip/postal_code = TW20 0EX Samples: 3 GSM128712: Thorlby_1-1_cold-acclimated_REP3_ATH1 GSM128713: Thorlby_1-2_3h-post-freeze_REP3_ATH1 GSM128714: Thorlby_1-3_24h-post-freeze_REP3_ATH1 154: GSE4933 record: Expression data from 7 day old Arabidopsis roots with 1h Red light or dark [Arabidopsis thaliana] Summary: Red light can affect a variety of responses in Arabidopsis. We characterize the early gene expression patterns of roots exposed to 1 hour of red light. Early genes indicate elements involved in photomorphogenesis, chloroplast development, PAL pathways, root hair development are regulated by 1 hour of red light We used microarrays to detail the gene expression underlying the effects of red light on roots. Samples: 6 GSM111156: 7d dark root 1h dark light, biological rep1 GSM111157: 7d dark root 1h red light, biological rep1 GSM111158: 7d dark root 1h dark light, biological rep2 GSM111159: 7d dark root 1h red light, biological rep2 GSM111160: 7d dark root 1h dark light, biological rep3 GSM111161: 7d dark root 1h red light, biological rep3 155: GSE5536 record: Response to CBF2 expression [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor CBF2. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Samples: 4 GSM128805: Zarka_3-1_MT-WSA_Rep1_ATH1 GSM128806: Zarka_3-2_MT-WSB_Rep2_ATH1 GSM128807: Zarka_3-3_MT-E24B_Rep1_ATH1 GSM128808: Zarka_3-4_MT-E2A_Rep1_ATH1 156: GSE5534 record: Response to cold, plate grown plants [Arabidopsis thaliana] Summary: This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in Col-0 plants grown in plates in response to low temperature over time. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Samples: 8 GSM128789: Zarka_1-1_MT-WT0HA_Rep1_ATH1 GSM128790: Zarka_1-2_MT-WT0HB_Rep2_ATH1 GSM128791: Zarka_1-3_MT-WT1HA_Rep1_ATH1 GSM128792: Zarka_1-4_MT-WT1HB_Rep2_ATH1 GSM128793: Zarka_1-5_MT-WT24HA_Rep1_ATH1 GSM128794: Zarka_1-6_MT-WT24HB_Rep2_ATH1 GSM128795: Zarka_1-7_MT-WT7DA_Rep1_ATH1 GSM128796: Zarka_1-8_MT-WT7DB_Rep2_ATH1 157: GSE5532 record: Responses to overexpression of wild type and constitutively active Arabidopsis MAP Kinase Kinase 2 [Arabidopsis thaliana] Summary: This experiment has been annotated by TAIR (http://arabidopsis.org). We examined transcript profiles triggered by three different arabidopsis R genes that recognize distinct Peronospora parasitica isolates. Experimenter name = Thomas Eulgem Experimenter phone = 43 1 4277 54622 Experimenter fax = 43 1 4277 9546 Experimenter department = Institute of Microbiology and Genetics Experimenter address = Institute of Microbiology and Genetics Experimenter address = Dr. Bohrgasse 9 Experimenter address = Vienna Experimenter zip/postal_code = A-1030 Experimenter country = Austria Samples: 3 GSM128775: Eulgem_1-1_Col-0-untreated_Rep1_AG GSM128776: Eulgem_1-3_Col-0-MKK2-w.t.4_Rep1_AG GSM128777: Eulgem_1-2_Col-0-MKK2-EE4_Rep1_AG 158: GSE5525 record: Transcriptome changes of Arabidopsis during pathogen and insect attack [Arabidopsis thaliana] Summary: Plant defenses against pathogens and insects are regulated differentially by cross-communicating signaling pathways in which salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) play key roles. To understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of SA, JA, and ET signaling in Arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack. Arabidopsis plants were exposed to a pathogenic leaf bacterium (Pseudomonas syringae pv. tomato), a pathogenic leaf fungus (Alternaria brassicicola), tissue-chewing caterpillars (Pieris rapae), cell-content-feeding thrips (Frankliniella occidentalis), or phloem-feeding aphids (Myzus persicae). Monitoring the signal signature in each plant-attacker combination showed that the kinetics of SA, JA, and ET production varies greatly in both quantity and timing. Samples: 14 GSM128715: Pieterse_1-1_Control-12h_Rep1_ATH1 GSM128716: Pieterse_1-2_Control-24h_Rep1_ATH1 GSM128717: Pieterse_1-3_Control-48h_Rep1_ATH1 GSM128718: Pieterse_1-4_Control-72h_Rep1_ATH1 GSM128719: Pieterse_1-5_avrPstDC3000-12h_Rep1_ATH1 GSM128720: Pieterse_1-6_avrPstDC3000-24h_Rep1_ATH1 GSM128721: Pieterse_1-7_Abrassicicola-24h_Rep1_ATH1 GSM128722: Pieterse_1-8_Abrassicicola-48h_Rep1_ATH1 GSM128723: Pieterse_1-9_Prapae-12h_Rep1_ATH1 GSM128724: Pieterse_1-10_Prapae-24h_Rep1_ATH1 GSM128725: Pieterse_1-11_Foccidentalis-24h_Rep1_ATH1 GSM128726: Pieterse_1-12_Foccidentalis-48h_Rep1_ATH1 GSM128727: Pieterse_1-13_Mpersicae-48h_Rep1_ATH1 GSM128728: Pieterse_1-14_Mpersicae-72h_Rep1_ATH1 159: GSE5465 record: Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes [Arabidopsis thaliana] Summary: 10-day-old wild-type and homozygous transgenic Arabidopsis seedlings (overexpressing OsTOP6A3 and OsTOP6B) grown under normal growth conditions were used for total RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol. Samples: 6 GSM125252: Seedling_wild-type_rep1 GSM125253: Seedling_wild-type_rep2 GSM125254: Seedling_OEA3L5_rep1 GSM125255: Seedling_OEA3L5_rep2 GSM125256: Seedling_OETOP6B_rep1 GSM125257: Seedling_OETOP6B_rep2 160: GSE5174 record: ETHYLENE-INSENSITIVE5 encodes a 5' to 3' exoribonuclease required for posttranscriptional regulation [Arabidopsis thaliana] Summary: Ethylene is a gaseous plant growth regulator that controls a multitude of developmental and stress responses. Recently, the levels of Arabidopsis EIN3 protein, a key transcription factor mediating ethylene-regulated gene expression, have been demonstrated to increase in response to the presence of ethylene gas. Furthern the absence ethylene, EIN3 is quickly degraded through a ubiquitin/proteasome pathway mediated by two F box proteins, EBF1 and EBF2 (1-3). Here, we report the identification of ETHYLENE INSENSITIVE5 as the 5??3? exoribonuclease XRN4. Specifically, we demonstrate that EIN5 is a component of the ethylene signal transduction cascade acting downstream of CTR1 that is required for ethylene-mediated gene expression changes. Furthere find that the ethylene insensitivity of ein5 mutant plants is a consequence of the over-accumulation of EBF1 and EBF2 mRNAs resulting in the under-accumulation of EIN3 even in the presence of ethylene gas. Samples: 12 GSM116725: ein2_air_1_polyA GSM116726: ein2_air_2_polyA GSM116727: ein2_ethylene_1_polyA GSM116728: ein2_ethylene_2_polyA GSM116729: ein5_air_1_polyA GSM116730: ein5_air_2_polyA GSM116731: ein5_ethylene_1_polyA GSM116732: ein5_ethylene_2_polyA GSM116733: wt_air_1_polyA GSM116734: wt_air_2_polyA GSM116735: wt_ethylene_1_polyA GSM116736: wt_ethylene_2_polyA 161: GSE5431 record: Expression profiling of A.thaliana with the posttranscriptionally silenced Myosin XI-K [Arabidopsis thaliana] Summary: This study was aimed to determine roles of individual myosins in organelle trafficking in plant cell. Expression of Myosin XI-K was suppressed in transgenic A.thaliana by using RNAi approach. To ensure that the RNAi-induced gene silencing was specific and did not affect expression of other myosins, a microarray analysis was performed. Samples: 4 GSM124351: A.thaliana expressing GUS transgene GSM124453: A.thaliana with the RNAi silenced Myosin XI-K, Group 1 GSM124460: A.thaliana with the RNAi silenced Myosin XI-K, Group 2 GSM124461: A.thaliana with the RNAi silenced Myosin XI-K, Group 3 162: GSE4662 record: STA1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover and stress tolerance [Arabidopsis thaliana] Summary: In plants, many gene transcripts are very unstable, which is important for the tight control of their temporal and spatial expression patterns. To identify cellular factors controlling the stability of unstable mRNAs in plants, we used luciferase imaging in Arabidopsis to isolate a recessive mutant, stabilized 1 (sta1), with enhanced stability of the normally unstable luciferase transcript. The sta1 mutation also causes the stabilization of some endogenous gene transcripts and has a range of developmental and stress response phenotypes. STA1 encodes a nuclear protein similar to the human U5 snRNP-associated 102-kDa protein and to the yeast pre-mRNA splicing factor Prp1p and Prp6p. STA1 expression is up-regulated by cold stress, and the sta1 mutant is defective in the splicing of the cold-induced COR15A gene. Samples: 7 GSM105203: Col-LUC_WT_no treatment_Rep1 GSM105204: Col-LUC_WT_no treatment_Rep2 GSM105205: sta1_no treatement_Rep1 GSM105206: sta1_no treatement_Rep2 GSM107670: C24-LUC_WT_no treatment_Rep5 GSM107711: Col-LUC_WT_no treatment_Rep3 GSM107712: Col-LUC_WT_no treatment_Rep4 163: GSE3811 record: Expression during deetioaltion under Rc in wt and phy mutant seedlings [Arabidopsis thaliana] Summary: Etiolated seedling response to one hour of continuous red light. Four-day-old dark-grown wild-type RLD and phyA101, phyB1 and phyAphyB mutant seedlings were transferred to Rc (680 nm, 8 mol m-2 s-1) for 1 h or retained in darkness as controls. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.RNA was extracted and subjected to expression analysis by using the Affymetrix ATH1 microarray containing approximately 22,000 Arabidopsis genes . SUBMITTER_CITATION: Tepperman JM, Hwang YS, Quail PH (2006). phyA dominates in transduction of red-light signals to rapidly-responding genes at the Initiation of Arabidopsis seedling deetiolation. Plant Journal 728-742. Samples: 24 GSM87413: 4 day seedling dark rep1_wildtype GSM87414: 4 day seedling dark rep2_wildtype GSM87415: 4 day seedling dark rep3_wildtype GSM87416: 4 day seedling dark rep1_phyA mutant GSM87417: 4 day seedling dark rep2_phyA mutant GSM87418: 4 day seedling dark rep3_phyA mutant GSM87419: 4 day seedling dark rep1_phyB mutant GSM87420: 4 day seedling dark rep2_phyB mutant GSM87421: 4 day seedling dark rep3_phyB mutant GSM87422: 4 day seedling dark rep1_phyAphyB mutant GSM87423: 4 day seedling dark rep2_phyAphyB mutant GSM87424: 4 day seedling dark rep3_phyAphyB mutant GSM87425: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_wildtype GSM87426: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_wildtype GSM87427: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_wildtype GSM87428: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_phyA mutant GSM87429: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_phyA mutant GSM87430: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_phyA mutant GSM87431: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_phyB mutant GSM87432: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_phyB mutant GSM87433: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_phyB mutant GSM87434: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_phyAphyB mutant GSM87435: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_phyAphyB mutant GSM87436: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_phyAphyB mutant 164: GSE4746 record: Expression data from Arabidopsis 14-day-old seedlings [Arabidopsis thaliana] Summary: Chitin, a polymer of N-acetyl-glucosamne, is a component of the cell walls of many plant fungal pathogens. During the infection process, the released chitin fragments (such as chitooctaose) from fungal cell walls by plant enzymes can trigger plant defense response and gene activation. The current work studies the regulation of Arabidopsis genes by the purified chitin fragment chitooctaose. We used the Affymetric Arabidopsis whole gene arrays to study the gene expression caused by chitin (chitooctaose). Samples: 6 GSM107437: Arabidopsis_Water-30M_rep1 GSM107438: Arabidopsis_Water-30M_rep2 GSM107439: Arabidopsis_Water-30M_rep3 GSM107440: Arabidopsis_Chitooctaose-30M_rep1 GSM107441: Arabidopsis_Chitooctaose-30M_rep2 GSM107442: Arabidopsis_Chitooctaose-30M_rep3 165: GSE4733 record: Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling [Arabidopsis thaliana] Summary: In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 hours following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are likely up-regulated during jasmonate-induced maturation. Samples: 27 GSM106825: opr3_0 hr_Rep1 GSM106827: opr3_0 hr_Rep2 GSM106828: opr3_0 hr_Rep3 GSM106833: opr3_JA_0.5 hr_Rep1 GSM106907: opr3_JA_0.5 hr_Rep2 GSM106908: opr3_JA_0.5 hr_Rep3 GSM106909: opr3-JA_2 hrs_Rep1 GSM106910: opr3_JA_2 hrs_rep2 GSM106911: opr2_JA_2 hrs_Rep3 GSM106912: opr3_JA 8hrs_Rep1 GSM106913: opr3_JA_8 hrs_Rep2 GSM106914: opr3_JA_8 hrs_Rep3 GSM106915: opr3_JA_22 hrs_Rep1 GSM106916: opr3_JA_22 hrs_Rep2 GSM106917: opr3_JA_22 hrs_Rep3 GSM106919: opr3_OPDA_0.5 hr_Rep1 GSM106920: opr3_OPDA_0.5 hr_Rep2 GSM106921: opr3_OPDA_0.5 hr_Rep3 GSM106922: opr3_OPDA_2 hrs_Rep1 GSM106923: opr3_OPDA_2 hrs_Rep2 GSM106924: opr3_OPDA_2 hrs_Rep3 GSM106934: opr3_OPDA_8 hrs_Rep1 GSM106966: opr3_OPDA_8 hrs_Rep3 GSM106967: opr3_OPDA_22 hrs_Rep1 GSM106969: opr3_OPDA_22 hrs_Rep2 GSM106970: opr3_OPDA_22 hrs_Rep3 GSM106973: ws_Rep1 166: GSE4638 record: Nep1 Treatment [Arabidopsis thaliana] Summary: In order to study the Nep1 responsive genes in Arabidopsis, experiments were performed with the Affymetrix GeneChip Arabidopsis ATH1 Genome Array (Santa Clara, CA; Cat # 900385). Samples: 4 GSM104362: Control Experiment 1 GSM104363: Control Experiment 2 GSM104364: Nep1 Experiment 1 GSM104365: Nep1 Experiment 2 167: GSE4021 record: effect of redox on gene expression [Arabidopsis thaliana] Summary: In this study, we used GC-MS analysis in combination with flux analysis and the Affymetrix ATH1 GeneChip to survey the metabolome and transcriptome of Arabidopsis leaves in response to manipulation of the thiol-disulfide status. Feeding low concentrations of the sulfhydryl reagent dithiothreitol (DTT) for one hour at the end of the dark period led to post-translational redox-activation of ADP-glucose pyrophosphorylase and major alterations in leaf carbon partitioning, including an increased flux into major respiratory pathways, starch- cell-wall-, and amino-acid synthesis and a reduced flux to sucrose. This was accompanied by a decrease in the levels of hexose-phosphates, while metabolites in the second half of the TCA cycle and various amino acids increased, indicating a stimulation of anaplerotic fluxes reliant on ?-ketoglutarate. Samples: 4 GSM91989: Leafdiscs_DTT_control1 GSM91990: Leafdiscs_DTT_treatment1 GSM91991: Leafdiscs_DTT_control2 GSM91992: Leafdiscs_DTT_treatment2 168: GSE3984 record: Difference in expression between SA- and mock-treated leaves 2 hours after application [Arabidopsis thaliana] Summary: Arabidopsis plants, ecotype Columbia, were sprayed with surfactant alone (0.01% Silwet) or surfactant and 1mM salicylic acid until all leaves were wet, 3 to 4 weeks after germination (before flowering). Leaves were harvested and frozen in liquid nitrogen. Three biological replicates were obtained over a period of 6 months. For each replicate, RNA was extracted using standard phenol/chloroform protocol and biotin-labeled cRNA was synthesized. cRNA was hybridized to 6 ATH1 GeneChip arrays. Cel files produced by the Affymetrix software were imported into R. Background subtraction, normalization and probe summaries were performed with the rma, quantile.normalization and median polish options of the rma function. Comparison of the SA- versus mock-treated tissue provides insight on the genes inv. Samples: 6 GSM90867: 2-hour mock-treated leaf material biological replicate 1 GSM90868: 2-hour mock-treated leaf material biological replicate 2 GSM90869: 2-hour mock-treated leaf material biological replicate 3 GSM90870: leaf material harvested 2 hours after spraying of 1 mM salicylic acid biological replicate 1 GSM90871: leaf material harvested 2 hours after spraying of 1 mM salicylic acid biological replicate 2 GSM90872: leaf material harvested 2 hours after spraying of 1 mM salicylic acid biological replicate 3 169: GSE4062 record: Heat shock response in Arabidopsis Hsa32 knockout mutant [Arabidopsis thaliana] Summary: Plants and animals share similar mechanisms in the heat-shock (HS) response, such as synthesis of the conserved HS proteins (Hsps). However, because plants are confined to a growing environment, in general they require unique features to cope with heat stress. We have analyzed the function of a novel Hsp, heat-stress-associated 32-kD protein (Hsa32), which is highly conserved in land plants but absent in most other organisms. The gene responds to HS at the transcriptional level in moss, Arabidopsis, and rice. Like other Hsps, Hsa32 protein accumulates greatly in Arabidopsis seedlings after HS treatment. Disruption of Hsa32 by T-DNA insertion does not affect growth and development under normal conditions. However, the acquired thermotolerance in the knockout line was compromised following a long recovery period (> 24 h) after an acclimation HS treatment, when a severe HS challenge killed the mutant but not the wild-type plants, but no significant difference was observed if they were challenged within a short recovery period. Samples: 8 GSM92823: Wt_shoot_control_rep1 GSM92824: Wt_shoot_control_rep2 GSM92825: Wt_shoot_heat shock_rep1 GSM92826: Wt_shoot_heat shock_rep2 GSM92827: Hsa32KO_shoot_control_rep1 GSM92828: Hsa32KO_shoot_control_rep2 GSM92829: Hsa32KO_shoot_heat shock_rep1 GSM92830: Hsa32KO_shoot_heat shock_rep2 170: GSE4113 record: Arabidopsis plants with altered levels of alternative oxidase [Arabidopsis thaliana] Summary: In higher plants, various developmental and environmental conditions enhance expression of the mitochondrial alternative oxidase (AOX). In this work transgenic Arabidopsis thaliana plants were generated that either overexpress AOX or inhibit its synthesis. Gene expression following antimycin A treatment, which inhibits the cytochrome pathway in mitochondria, was studied in an AOX overexpressor line. The role of AOX in regulation of reactive oxygen species (ROS) in leaves was studied in the transgenic lines. The transgenic lines were also used to investigate the mitochondria-chloroplasts interaction in assays performed at three-times growth light. For most of the parameters measured AOX antisense lines and WT plants showed a very similar response whereas AOX sense lines differed in several aspects. Samples: 9 GSM94006: Wild type first repeat GSM94007: A1-1 first repeat GSM94008: A1-1 second repeat GSM94009: A1-1 third repeat GSM94010: Wild type third repeat GSM94011: S5 third repeat GSM94012: Wild type second repeat GSM94013: S5 first repeat GSM94014: S5 second repeat 171: GSE3847 record: Tropic-stimulus induced changes in gene expression [Arabidopsis thaliana Brassica oleracea] Summary: Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny-Went theory Went, F.W. & Thimann, K.V. Phytohormones (1937) (Macmillan, New York) predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet, the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Samples: 15 GSM87736: 2hr shaded replicate 1 GSM87737: 2hr shaded replicate 2 GSM87738: 2hr shaded replicate 3 GSM87739: 2hr lit replicate 1 GSM87740: 2hr lit replicate 2 GSM87741: 2hr lit replicate 3 GSM87742: 2hr bottom replicate1 GSM87743: 2hr bottom replicate 2 GSM87744: 2hr bottom replicate 3 GSM87745: 2hr top replicate 1 GSM87746: 2hr top replicate 2 GSM87747: 2hr top replicate 3 GSM87748: unstimulated control replicate 1 GSM87749: unstimulated control replicate 2 GSM87750: unstimulated control replicate 3 172: GSE3959 record: RNA changes induced by LEAFY COTYLEDON2 activity in Arabidopsis seedlings [Arabidopsis thaliana] Summary: LEAFY COTYLEDON2 activity was induced via a LEC2-Glucocorticoid Receptor fusion protein in Arabidopsis seedlings. Samples: 8 GSM90292: Transgenic LEC2GR Seedling 0h Dex 1 GSM90293: Transgenic LEC2GR Seedling 0h Dex 2 GSM90294: Transgenic LEC2GR Seedling 1h Dex 1 GSM90295: Transgenic LEC2GR Seedling 1h Dex 2 GSM90296: Transgenic LEC2GR Seedling 4h Dex 1 GSM90297: Transgenic LEC2GR Seedling 4h Dex 2 GSM90298: Wild-Type WS-O Seedling 4h Dex 1 GSM90299: Wild-Type WS-O Seedling 4h Dex 2 173: GSE3279 record: Gain-of-function mutants of SOC1 vs soc1-2 [Arabidopsis thaliana] Summary: To find downstream target of SOC1, we attemted global expression profiles in gain-of-function mutants of SOC1 To find downstream target of SOC1, we attemted global expression profiles in soc1-101D: Expt. 1 GSM73643, GSM73646 Expt. 2 GSM73647, GSM73648 Expt. 3 GSM73649, GSM73650 To find downstream target of SOC1, we attemted global expression profiles in soc1-2: GSM73649, GSM73651 To find downstream target of SOC1, we attemted global expression profiles in gain-of-function mutants of SOC1: GSM73643, GSM73646, GSM73647, GSM73648, GSM73649, GSM73650 Samples: 7 GSM73643: Col_Experiment 1 GSM73646: soc1-101D_Experiment 1 GSM73647: Col_Experiment 2 GSM73648: soc1-101D_Experiment 2 GSM73649: Col_Experiment 3 GSM73650: soc1-101D_Experiment 3 GSM73651: soc1-2_Experiment 3 174: GSE3865 record: CSN4-1 mutant analysis [Arabidopsis thaliana] Summary: Transcript profiling analysis of csn4-1 light grown mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array Samples: 6 GSM88049: csn4-1_mutant replicate 1 GSM88050: csn4-1_mutant replicate 2 GSM88051: csn4-1_mutant replicate 3 GSM88055: CSN4-1 wild type replicate 1 GSM88056: CSN4 wild type replicate 2 GSM88057: CSN4-1 wild type replicate 3 175: GSE3864 record: AtFBP7 mutant analysis [Arabidopsis thaliana] Summary: Transcript profiling analysis of AtFBP7 mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array. Samples: 6 GSM88043: AtFBP7 wild type replicate 1 GSM88044: AtFBP7 wild type replicate 2 GSM88045: AtFBP7 wild type replicate 3 GSM88052: AtFBP7 mutant replicate 1 GSM88053: AtFBP7 mutant replicate 2 GSM88054: AtFBP7 mutant replicate 3 176: GSE3863 record: VFB mutant analysis [Arabidopsis thaliana] Summary: Transcript profiling analysis of vfb (Vier F-Box) mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array. Samples: 6 GSM88040: VFB wild type replicate 1 GSM88041: VFB wild type replicate 2 GSM88042: VFB wild type replicate 3 GSM88046: VFB_mutant replicate 1 GSM88047: VFB_mutant replicate 2 GSM88048: VFB_mutant replicate 3 177: GSE3799 record: Histone acetylation during seed germination [Arabidopsis thaliana] Summary: This SuperSeries is composed of the following subset Series: GSE3783: Trichostatin A (TSA) inhibition of histone deacetylase in Arabiodopsis thaliana GSE3784: Seed germination in presence and absence of histone deaceatylase inhibitor, Trichostain A (TSA). Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. 2 related Platforms Samples: 7 GSM86644: Imbibed seed_TSA_3days_rep1 GSM86677: Imbibed seed_TSA_3days_rep2 GSM86739: Imbibed seed_untreated_3days_rep1 GSM86741: Imbibed seed_untreated_3days_rep2 GSM86743: Unimbibed seed GSM86744: Imbibed seeds_3day GSM86745: Imbibed seeds_3days_TSA 178: GSE3784 record: Seed germination in presence and absence of histone deaceatylase inhibitor, Trichostain A (TSA). [Arabidopsis thaliana] Summary: Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. Samples: 3 GSM86743: Unimbibed seed GSM86744: Imbibed seeds_3day GSM86745: Imbibed seeds_3days_TSA 179: GSE3704 record: Effects of a 6h-long treatment with 90 mM sucrose to 4-d old, dark grown Arabidopsis seedlings [Arabidopsis thaliana] Summary: Dark grown Arabidopsis seedlings (Columbia gl1) were grown in the dark at 23°C for 4 days before adding 90 mM sucrose for 6h. Samples: 4 GSM38613: AIR EXPERIMENT 1 GSM38614: AIR EXPERIMENT 2 GSM85538: Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 1 GSM85539: Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 2 180: GSE630 record: Auxin-mediated gene expression [Arabidopsis thaliana] Summary: Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Samples: 60 GSM9571: Col_control_1 GSM9572: Col_control_2 GSM9573: Col_control_3 GSM9574: Col_+IAA_1 GSM9575: Col_+IAA_2 GSM9576: Col_+IAA_3 GSM9577: nph4-1_control_1 GSM9578: nph4-1_control_2 GSM9579: nph4-1_control_3 GSM9580: nph4-1_+IAA_1 GSM9581: nph4-1_+IAA_2 GSM9582: nph4-1_+IAA_3 GSM9583: arf19-1_control_1 GSM9584: arf19-1_control_2 GSM9585: arf19-1_control_3 GSM9586: arf19-1_+IAA_1 GSM9587: arf19-1_+IAA_2 GSM9588: arf19-1_+IAA_3 GSM9589: nph4-1arf19-1_control_1 GSM9590: nph4-1arf19-1_control_2 GSM9591: nph4-1arf19-1_control_3 GSM9592: nph4-1arf19-1_+IAA_1 GSM9593: nph4-1arf19-1_+IAA_2 GSM9594: nph4-1arf19-1_+IAA_3 GSM9595: Col_control_I_1 GSM9596: Col_control_I_2 GSM9597: Col_control_I_3 GSM9598: Col_+IAA_I_1 GSM9599: Col_+IAA_I_2 GSM9600: Col_+IAA_I_3 GSM9601: iaa17-6_control_1 GSM9602: iaa17-6_control_2 GSM9603: iaa17-6_control_3 GSM9605: iaa17-6_+IAA_1 GSM9606: iaa17-6_+IAA_2 GSM9607: iaa17-6_+IAA_3 GSM9608: arx3-1_control_1 GSM9609: axr3-1_control_2 GSM9610: axr3-1_control_3 GSM9611: axr3-1_+IAA_1 GSM9612: axr3-1_+IAA_2 GSM9613: axr3-1_+IAA_3 GSM9614: i5i6i19_control_1 GSM9615: i5i6i19_control_2 GSM9616: i5i6i19_control_3 GSM9617: i5i6i19_+IAA_1 GSM9618: i5i6i19_+IAA_2 GSM9619: i5i6i19_+IAA_3 GSM9620: Col_control_A2_1 GSM9624: Col_+IAA_A2_1 GSM9625: Col_control_A2_2 GSM9626: Col_+IAA_A2_2 GSM9627: Col_control_A2_3 GSM9628: Col_+IAA_A2_3 GSM9629: arf2-6_control_1 GSM9630: arf2-6_+IAA_1 GSM9631: arf2-6_control_2 GSM9632: arf2-6_+IAA_2 GSM9633: arf2-6_control_3 GSM9634: arf2-6_+IAA_3 181: GSE3416 record: Diurnal gene expression in Arabidopsis thaliana Col-0 rosette leaves [Arabidopsis thaliana] Summary: How do the transcript levels of leaf-expressed genes change in a normal day-night cycle? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rythm at 20°C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested at 6 timepoints every 4 hours beginning with the end of the night (still in darkness). Samples: 18 GSM77055: 00h Col-0 replicate A GSM77056: 00h Col-0 replicate B GSM77057: 00h Col-0 replicate C GSM77058: 04h Col-0 replicate A GSM77059: 04h Col-0 replicate B GSM77060: 04h Col-0 replicate C GSM77061: 08h Col-0 replicate A GSM77062: 08h Col-0 replicate B GSM77063: 08h Col-0 replicate C GSM77064: 12h Col-0 replicate A GSM77065: 12h Col-0 replicate B GSM77066: 12h Col-0 replicate C GSM77067: 16h Col-0 replicate A GSM77068: 16h Col-0 replicate B GSM77069: 16h Col-0 replicate C GSM77070: 20h Col-0 replicate A GSM77071: 20h Col-0 replicate B GSM77072: 20h Col-0 replicate C 182: GSE3533 record: UV-B induced genes in wild-type Arabidopsis versus mutants uvr8-1 and hy5-1 using Affymetrix ATH1 array [Arabidopsis thaliana] Summary: This experiment tests the effect of physiological dose of UV-B radiation on wild-type and uvr8-1 (UV Resistance Locus 8) and hy5-1 transcription factor mutants of Arabidopsis. Samples: 15 GSM81005: Arabidopsis_leaf_wildtype_in_white_light_rep1 GSM81006: Arabidopsis_leaf_wildtype_in_white_light_rep2 GSM81007: Arabidopsis_leaf_wildtype_in_white_light_rep3 GSM81008: Arabidopsis_leaf_wildtype_in_UV-B_light_rep1 GSM81009: Arabidopsis_leaf_wildtype_in_UV-B_light_rep2 GSM81010: Arabidopsis_leaf_wildtype_in_UV-B_light_rep3 GSM81011: Arabidopsis_leaf_uvr8-1_mutant_in_white_light_rep1 GSM81012: Arabidopsis_leaf_uvr8-1_mutant_in_white_light_rep2 GSM81013: Arabidopsis_leaf_uvr8-1_mutant_in_white_light_rep3 GSM81014: Arabidopsis_leaf_uvr8-1_mutant_in_UV-B_light_rep1 GSM81015: Arabidopsis_leaf_uvr8-1_mutant_in_UV-B_light_rep2 GSM81016: Arabidopsis_leaf_uvr8-1_mutant_in_UV-B_light_rep3 GSM81017: Arabidopsis_leaf_hy5-1_mutant_in_UV-B_light_rep1 GSM81018: Arabidopsis_leaf_hy5-1_mutant_in_UV-B_light_rep2 GSM81019: Arabidopsis_leaf_hy5-1_mutant_in_UV-B_light_rep3 183: GSE3709 record: Cell culture treatment study [Arabidopsis thaliana] Summary: Profiling the transcriptome of Arabidopsis suspension cells in response to a range of abiotic treatments. Samples: 37 GSM85626: hydrogen peroxide treated, 3 h, replicate 1 GSM85627: hydrogen peroxide treated, 3 h, replicate 2 GSM85628: mannitol treated, 3 h, replicate 1 GSM85629: 0.125 uM oligomycin treated, 3 h, replicate 1 GSM85630: 0.125 uM oligomycin treated, 3 h, replicate 2 GSM85631: 1.25 uM oligomycin treated, 3 h, replicate 1 GSM85632: 1.25 uM oligomycin treated, 3 h, replicate 2 GSM85633: chitin treated, 3 h, replicate 1 GSM85634: chitin treated, 3 h, replicate 2 GSM85635: chloramphenicol treated, 3 h, replicate 1 GSM85636: chloramphenicol treated, 3 h, replicate 2 GSM85637: cold treated, 3 h, replicate 1 GSM85638: cold treated, 3 h, replicate 2 GSM85639: untreated 3 h replicate 1 GSM85640: untreated 3 h replicate 2 GSM85641: untreated 3 h replicate 3 GSM85642: untreated 3 h replicate 4 GSM85643: flagellen treated, 3 h, replicate 1 GSM85644: flagellen treated, 3 h, replicate 2 GSM85645: treated with N2 to replace air, 3 h, replicate 1 GSM85646: treated with N2 gas to replace air, 3 h, replicate 2 GSM85647: rotenone treated, 3 h, replicate 1 GSM85648: rotenone treated, 3 h, replicate 2 GSM85649: 10 uM salicylic acid treated, 3 h, replicate 1 GSM85650: 10 uM salicylic acid treated, 3 h, replicate 2 GSM85651: 100 uM salicylic acid treated, 3 h, replicate 1 GSM85652: 100 uM salicylic acid treated, 3 h, replicate 2 GSM85653: untreated 12 h replicate 1 GSM85654: untreated 12 h replicate 2 GSM85655: rotenone treated, 12 h, replicate 1 GSM85656: rotenone treated, 12 h, replicate 2 GSM85657: norflurazon treated, 12 h, replicate 1 GSM85658: norflurazon treated, 12 h, replicate 2 GSM85659: chloramphenicol treated, 12 h, replicate 1 GSM85660: chloramphenicol treated, 12 h, replicate 2 GSM85661: cysteine treated, 12 h, replicate 1 GSM85662: cysteine treated, 12 h, replicate 2 184: GSE3424 record: Diurnal gene expression in rosette leaves of the phosphoglucomutase mutant (Col-0) [Arabidopsis thaliana] Summary: How do transcript levels of leaf-expressed genes change in a normal day-night cycle of the phosphoglucomutase (pgm) mutant? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rhythm at 20°C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested in series at 6 times every 4 hours, beginning with the end of the night (still in darkness). Samples: 8 GSM77181: 00h pgm (Col-0) mutant replicate A GSM77182: 00h pgm (Col-0) mutant replicate B GSM77183: 04h pgm (Col-0) mutant replicate A GSM77184: 08h pgm (Col-0) mutant replicate A GSM77185: 12h pgm (Col-0) mutant replicate A GSM77186: 12h pgm (Col-0) mutant replicate B GSM77187: 16h pgm (Col-0) mutant replicate A GSM77188: 20h pgm (Col-0) mutant replicate A 185: GSE3423 record: Carbon fixation (endogenous sugar) and light-dependent gene expression [Arabidopsis thaliana] Summary: Internal sugar and light specific dependent regulation of leaf gene expression was addressed by changing [CO2] to lower than compensation point [CO2] in combination with light or prolonged darkness. Plants were grown on soil in a 12/12 h light/dark rhythm at 20°C day and night and under normal [CO2]. 5 weeks after germination, the above-ground rosettes of the non-flowering plants were harvested, 12 plants per sample. Plants were harvested 4hrs after the end of night (i) under low (< 50 ppm) [CO2] and 150 µE fluorescent light , (ii) under normal [CO2] and light, and, (iii) under low [CO2] and prolonged darkness. The low [CO2] treatment started 30 min before the end of night and stopped with harvesting. Samples: 6 GSM77175: 04h low CO2 + light replicate A GSM77176: 04h normal CO2 + light replicate A GSM77177: 04h low CO2 + dark replicate A GSM77178: 04h low CO2 + light replicate B GSM77179: 04h normal CO2 + light replicate B GSM77180: 04h low CO2 + dark replicate B 186: GSE3454 record: Transcriptome analysis of ROP10 GTPase-mediated abscisic acid (ABA) signaling in Arabidopsis [Arabidopsis thaliana] Summary: In this study, we have identified genes that are respectively activated and repressed by the low concentration of ABA and show that ROP10 gates a specific subset of genes that are responsive only to a low ABA concentration. Samples: 12 GSM78332: Ws wild-type, no ABA control, replicate 1 GSM78333: Ws wild-type, no ABA control, replicate 2 GSM78334: Ws wild-type, no ABA control, replicate 3 GSM78335: rop10-1 mutant, no ABA control, replicate 1 GSM78336: rop10-1 mutant, no ABA control, replicate 2 GSM78337: rop10-1 mutant, no ABA control, replicate 3 GSM78338: Ws wild-type, 1µM ABA treatment, replicate 1 GSM78339: Ws wild-type, 1µM ABA treatment, replicate 2 GSM78340: Ws wild-type, 1µM ABA treatment, replicate 3 GSM78341: rop10-1 mutant, 1µM ABA treatment, replicate 1 GSM78342: rop10-1 mutant, 1µM ABA treatment, replicate 2 GSM78343: rop10-1 mutant, 1µM ABA treatment, replicate 3 187: GSE3350 record: SLR/IAA14-dependent auxin induced lateral root initiation [Arabidopsis thaliana] Summary: Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. Samples: 14 GSM75508: Col-0 0h NAA replicate 1 GSM75509: Col-0 2h NAA replicate 1 GSM75510: Col-0 6h NAA replicate 1 GSM75511: Col-0 6h MOCK replicate 1 GSM75512: Col-0 0h NAA replicate 2 GSM75513: Col-0 2h NAA replicate 2 GSM75514: Col-0 6h NAA replicate 2 GSM75515: Col-0 6h MOCK replicate 2 GSM75516: slr-1 0h NAA replicate 1 GSM75517: slr-1 2h NAA replicate 1 GSM75518: slr-1 6h NAA replicate 1 GSM75519: slr-1 0h NAA replicate 2 GSM75520: slr-1 2h NAA replicate 2 GSM75521: slr-1 6h NAA replicate 2 188: GSE631 record: Auxin mediated gene expression in WT and arf2-6 mutant [Arabidopsis thaliana] Summary: Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations. Data analysis: Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The ?R? environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Samples: 12 GSM9620: Col_control_A2_1 GSM9624: Col_+IAA_A2_1 GSM9625: Col_control_A2_2 GSM9626: Col_+IAA_A2_2 GSM9627: Col_control_A2_3 GSM9628: Col_+IAA_A2_3 GSM9629: arf2-6_control_1 GSM9630: arf2-6_+IAA_1 GSM9631: arf2-6_control_2 GSM9632: arf2-6_+IAA_2 GSM9633: arf2-6_control_3 GSM9634: arf2-6_+IAA_3 189: GSE3326 record: ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome [Arabidopsis thaliana] Summary: To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes. For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h. A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated. A large number of the early cold-responsive genes encode transcription factors that likely control late-responsive genes, which implies a multitude of transcriptional cascades. In addition, many genes involved in post-transcriptional and chromatin level regulation were also cold regulated suggesting their involvement in cold responsive gene regulation. Samples: 16 GSM74894: Wildtype_no treatment_Rep1 GSM74895: Wildtype_no treatment_Rep2 GSM74896: Wildtype_3H Cold_Rep1 GSM74897: Wildtype_3H Cold_Rep2 GSM74898: Wildtype_6H Cold_Rep1 GSM74899: Wildtype_6H Cold_Rep2 GSM74900: Wildtype_24H Cold_Rep1 GSM74901: Wildtype_24H Cold_Rep2 GSM74902: ice1_no treatment_Rep1 GSM74903: ice1_no treatment_Rep2 GSM74904: ice1_3H Cold_Rep1 GSM74905: ice1_3H Cold_Rep2 GSM74906: ice1_6H Cold_Rep1 GSM74907: ice1_6H Cold_Rep2 GSM74908: ice1_24H Cold_Rep1 GSM74909: ice1_24H Cold_Rep2 190: GSE2169 record: rre1 and rre2 mutants [Arabidopsis thaliana] Summary: Effect of chitin on rre-1 and rre-2 seedlings. Supplementary Files: CEL CHP EXP download... Samples: 24 GSM39191: RRE1_C1 GSM39192: RRE1_C2 GSM39193: RRE1_C3 GSM39194: RRE1_C4 GSM39195: RRE1_Chitin1 GSM39196: RRE1_Chitin2 GSM39197: RRE1_Chitin3 GSM39198: RRE1_Chitin4 GSM39199: Col_C1 GSM39200: Col_C2 GSM39201: Col_C3 GSM39202: Col_C4 GSM39203: Col_Chitin1 GSM39204: Col_Chitin2 GSM39205: Col_Chitin3 GSM39206: Col_Chitin4 GSM39207: RRE2_C1 GSM39208: RRE2_C2 GSM39209: RRE2_C3 GSM39210: RRE2_C4 GSM39211: RRE2_Chitin1 GSM39212: RRE2_Chitin2 GSM39213: RRE2_Chitin3 GSM39214: RRE2_Chitin4 191: GSE3011 record: DCL4 Functional Analysis [Arabidopsis thaliana] Summary: Rosette leaves (5-8) and inflorescence stages (1-12) from dcl1-7, rdr6-15, and dcl4-2 mutants, involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and trans-acting siRNAs). Samples: 27 GSM65917: CD4R6D1_L-1 GSM65918: CD4R6D1_L-2 GSM65919: CD4R6D1_L-3 GSM65920: CD4R6D1_L-4 GSM65921: CD4R6D1_L-5 GSM65922: CD4R6D1_L-6 GSM65923: CD4R6D1_L-7 GSM65924: CD4R6D1_L-8 GSM65925: CD4R6D1_L-9 GSM65926: CD4R6D1_L-10 GSM65927: CD4R6D1_L-11 GSM65928: CD4R6D1_L-12 GSM65929: CD4R6D1_I-13 GSM65930: CD4R6D1_I-14 GSM65931: CD4R6D1_I-15 GSM65932: CD4R6D1_I-16 GSM65933: CD4R6D1_I-17 GSM65934: CD4R6D1_I-18 GSM65935: CD4R6D1_I-19 GSM65936: CD4R6D1_I-20 GSM65937: CD4R6D1_I-21 GSM65938: CD4R6D1_I-22 GSM65939: CD4R6D1_I-23 GSM65940: CD4R6D1_I-24 GSM65941: CD4R6D1_I-25 GSM65942: CD4R6D1_I-26 GSM65943: CD4R6D1_I-27 192: GSE3220 record: Arabidopsis pen3 mutant and wild type Col-O comparison under host inoculation, nonhost inoculation and no inoculation. [Arabidopsis thaliana] Summary: Arabidopsis is a host to the fungal powdery mildew pathogen, Erysiphe cichoracearum, and a nonhost to Blumeria graminis f.sp. hordei, the powdery mildew pathogenic on barley. A screen for mutants that allowed increased entry by this inappropriate or nonhost pathogen on Arabidopsis led to the identification of PEN3. While pen3 mutants permitted both increased penetration and increased hyphal growth by B. g. hordei, they were unexpectedly resistant to E. cichoracearum. This resistance was correlated with the appearance of chlorotic patches and was salicylic acid-dependent. Consistent with this observation, microarray analysis revealed that the salicylic acid defense pathway was hyper-induced in pen3 relative to wild type following inoculation with either E. cichoracearum or B. g. hordei. The pen3 phenotypes result from a loss of function of AtPDR8, a ubiquitously and highly expressed ATP binding cassette transporter. Samples: 24 GSM70995: Col_Bgh1 GSM70996: Col_Bgh2 GSM70997: Col_Bgh3 GSM70998: Col_Ec1 GSM70999: Col_Ec2 GSM71000: Col_Ec3 GSM71001: Col_Ec4 GSM71002: Col_Un1 GSM71003: Col_Un2 GSM71004: Col_Un3 GSM71005: Col_Un4 GSM71006: pen3_Bgh1 GSM71007: pen3_Bgh2 GSM71008: pen3_Bgh3 GSM71009: pen3_Bgh4 GSM71010: pen3_Ec1 GSM71011: pen3_Ec2 GSM71012: pen3_Ec4 GSM71013: pen3_Un1 GSM71014: pen3_Un2 GSM71015: pen3_Un3 GSM71016: pen3_Un4 GSM71017: Col_Bgh4 GSM71018: pen3_Ec3 193: GSE3038 record: ATH1 Transcriptome profiling of dark grown photoreceptor mutants seedlings of Arabidopsis [Arabidopsis thaliana] Summary: Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. Samples: 8 GSM65896: WTdarkcol1 ATH1 GSM65897: WTDARK2col ATH1 GSM65898: PHYADARK ATH1 GSM65902: PHYADARK2 ATH1 GSM65904: PHYBDARK1 ATH1 GSM65910: PHYBDARK2 ATH1 GSM66029: PHYAPHYBDARK1 ATH1 GSM66030: PHYAPHYBDARK2 ATH1 194: GSE3002 record: Transcriptome profiling of dark grown photoreceptor mutants seedlings of Arabidopsis ATH1 [Arabidopsis thaliana] Summary: Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. Samples: 4 GSM65294: WTD ATH1 GSM65295: WTDARK2 ATH1 GSM65296: phyAphyBdark1 ATH1 GSM65297: PHYAPHYBDARK 2 ATH1 195: GSE3056 record: Arabidopsis Pollination Study [Arabidopsis thaliana] Summary: Microarray experiments were used to build a profile of candidate stigma genes that facilitate early pollination events. Of over 24,000 genes probed, we identified 11,403 genes expressed in stigma tissue, 317 of these that are stigma specific (not expressed in control tissues). To appear in Sexual Plant Reproduction, Swanson, Clark, and Preuss, "Expression Profiling of Arabidopsis Stigma Tissue Identifies Stigma-Specific Genes." Supplementary Files: CEL CHP DAT EXP RPT download... Samples: 11 GSM67078: Arabidopsis_Ovary01 GSM67079: Arabidopsis_Ovary02 GSM67080: Arabidopsis_Ovary03 GSM67081: Arabidopsis_Ovary04 GSM67082: Arabidopsis_Seedling01 GSM67083: Arabidopsis_Seedling02 GSM67084: Arabidopsis_Stigma01 GSM67086: Arabidopsis_Stigma02 GSM67087: Arabidopsis_Stigma03 GSM67110: Arabidopsis_Seedling03 GSM67112: Arabidopsis_Seedling04 196: GSE2848 record: Auxin Response Factor mediated flower gene expression [Arabidopsis thaliana] Summary: The aim of this study was to examine the contribution of ARF6 and ARF8 to flower gene expression. Flowers from arf6 arf8 plants undergo a developmental arrest at approximately stage 12, just prior to flower opening. Flowers from wild-type, ARF6/arf6 arf8/arf8, and arf6 arf8 plants were separated into stage 1-10 flowers, stage 11+12 flowers, and stage 13-14 flowers to define the developmental stages at which ARF6 and ARF8 are required for gene expression. Samples: 12 GSM62694: Columbia flowers_stage 1-10 GSM62695: Columbia flowers_stage 11-12 GSM62696: Columbia flowers_stage 13-14 GSM62697: Columbia_stem GSM62698: arf6/arf6 ARF8/arf8 flowers_stage 1-10 GSM62699: arf6/arf6 ARF8/arf8 flowers_stage 11-12 GSM62700: arf6/arf6 ARF8/arf8 flowers_stage 13-14 GSM62701: arf6/arf6 ARF8/arf8_stem GSM62702: arf6 arf8 flowers_stage 1-10 GSM62703: arf6 arf8 flowers_stage 11-12 GSM62704: arf6 arf8 flowers_stage 13-14 GSM62705: arf6 arf8_stem 197: GSE2847 record: Auxin induction in wild type and arf6 arf8 flowers [Arabidopsis thaliana] Summary: The aim of this study was to examine the roles of Auxin Response Factors (ARFs) in flower gene expression. Flowers from arf6 arf8 plants undergo a developmental arrest at approximately stage 12, just prior to flower opening. Wild-type, ARF6/arf6 arf8/arf8, and arf6 arf8 plants were treated with 10 uM indole-3-acetic acid for thirty minutes to identify genes that respond rapidly to auxin in an ARF6/ARF8-dependent manner. Samples: 7 GSM62687: Columbia flowers_stage 1-14_untreated GSM62688: Columbia flowers_stage 1-14_IAA GSM62689: Columbia flowers_stage 1-14_mock GSM62690: arf6/arf6 ARF8/arf8 flowers_stage 1-14_untreated GSM62691: arf6/arf6 ARF8/arf8 flowers_stage 1-14_IAA GSM62692: arf6 arf8 flowers_stage 1-14_untreated GSM62693: arf6 arf8 flowers_stage 1-14_IAA 198: GSE2538 record: Chitin Oligomer Experiment [Arabidopsis thaliana] Summary: Using the ATH1 Affymetrix microarrays consisting of about 23,000 genes, we examined the response of Arabidopsis seedlings to chito-tetramers, chito-octamers and hydrolyzed chitin after 30 min of treatment. Keywords = chitin Keywords = defense Keywords = elicitor Keywords = mutant Keywords = powdery mildew Keywords = Erysiphe cichoracearum Samples: 9 GSM48122: Col_8mer1 GSM48123: Col_8mer2 GSM48124: Col_8mer3 GSM48125: Col_CSC1 GSM48126: Col_CSC2 GSM48127: Col_CSC3 GSM48128: Col_Mock1 GSM48129: Col_Mock2 GSM48130: Col_Mock3 199: GSE2218 record: Changes in transcript abundance and association with large polysomes in response to hypoxia stress [Arabidopsis thaliana] Summary: 7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes. TABLE 1 - Comparison between transcript abundance in non-stress and hypoxia-stress conditions. TABLE 2 - Comparison between transcript abundance in large polysome complexes (5 or bosomes per mRNA) in non-stress and 12 hypoxia-stress conditions. TABLE 3 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under non-stress conditions. Raw data (not normalized) TABLE 4 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under 12h of hypoxia-stress. Samples: 4 GSM40552: Total RNA, non-stressed GSM40553: Total RNA - hypoxia stress GSM40554: Polysomal mRNA, non-stress GSM40555: Polysomal mRNA - Hypoxia stress 200: GSE2696 record: Brassinosteroid mutant (bzr1-1D and det2) analysis [Arabidopsis thaliana] Summary: Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth and development of plants. BR signaling through cell-surface receptor kinases and intracellular components leads to dephosphorylation and accumulation of the nuclear protein BZR1. How BR signaling regulates gene expression, however, remains unknown. Here we show that BZR1 is a transcriptional repressor that has a previously unknown DNA binding domain and binds directly to the promoters of feedback-regulated BR biosynthetic genes. To identify additional BZR1-regulated genes and to understand the BR-regulated transcriptional pathways, we examined the effects of bzr1-1D and det2 mutations on the expression of BR-regulated genes by using the Arabidopsis full-genome oligo microarray (Affymetrix). Microarray analyses id. Samples: 6 GSM41198: bzr1-1D_Mock1 GSM41199: bzr1-1D_Mock2 GSM41200: bzr1-1D_Mock3 GSM41201: det2_Mock1 GSM41202: det2_Mock2 GSM41203: det2_Mock3 201: GSE2473 record: Small RNA biogenesis mutants [Arabidopsis thaliana] Summary: Inflorescence stages 1 to 12 from mutants involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and siRNAs). Supplementary Files: CEL CHP RPT download... Samples: 44 GSM47011: Col-0 1 GSM47012: Col-0 2 GSM47013: Col-0 3 GSM47014: Ler 4 GSM47015: Ler 5 GSM47016: Ler 6 GSM47017: Ler 7 GSM47018: Ler 8 GSM47019: Ler 9 GSM47020: Col-0 10 GSM47021: Col-0 11 GSM47022: Col-0 12 GSM47023: dcl1-7 13 GSM47024: dcl1-7 14 GSM47025: dcl1-7 15 GSM47026: dcl1-7 16 GSM47027: dcl1-7 17 GSM47028: dcl2-1 18 GSM47029: dcl2-1 19 GSM47030: dcl2-1 20 GSM47031: dcl3-121 GSM47032: dcl3-1 22 GSM47033: dcl3-1 23 GSM47034: hen1 24 GSM47035: hen1 25 GSM47036: hen1 26 GSM47037: hst-15 27 GSM47038: hst-15 28 GSM47039: hst-15 29 GSM47040: hyl1 30 GSM47041: hyl1 31 GSM47042: hyl1 32 GSM47043: rdr1-1 33 GSM47044: rdr1-1 34 GSM47045: rdr1-1 35 GSM47046: rdr2-1 36 GSM47047: rdr2-1 37 GSM47048: rdr2-1 38 GSM47049: Col-0 39 GSM47050: Col-0 40 GSM47051: Col-0 41 GSM47052: rdr6-15 42 GSM47053: rdr6-15 43 GSM47054: rdr6-15 44 202: GSE2406 record: WTv.AOXantisense [Arabidopsis thaliana] Summary: Leaf transcriptome comparison of untransformed Col-0 Arabidopsis plants with plants transformed to be anti-sense for AtAOX1a (alternative oxidase). Two ?bio-replicates? were sampled, for a total of four microarray chips?Col-0 and anti-sense leaf tissue from a first planting (samples GSM45208 and GSM45231, respectively), and from a second planting made one week later (samples GSM45209 and GSM45278, respectively). See sample descriptions for growth conditions and microarray procedure. Keywords = alternative oxidase Keywords = plant mitochondria Keywords = respiration Keywords = leaves Supplementary Files: CEL RPT TXT download... Samples: 4 GSM45208: 00304WT_1 GSM45209: 00304WT_2 GSM45231: 00304AS12_1 GSM45278: 00304AS12_2 203: GSE1766 record: Time course of Arabidopsis seedlings treated with 6-Benzyl adenine [Arabidopsis thaliana] Summary: Time course of Arabidopsis seedlings treated with 6-Benzyl adenine dissolved in diluted KOH for 15 min or 2 hours Samples: 13 GSM27375: Col-0 BA 0 #1 GSM27376: Col-0 BA 15 #1 GSM27377: Col-0 BA 120 #1 GSM28436: Col-0 BA 0 #2 GSM28437: Col-0 BA 15 #2 GSM28438: Col-0 BA 120 #2 GSM28439: CKX1 BA 0 #1 GSM28440: CKX1 BA 15 #1 GSM28441: CKX1 BA 0 #2 GSM28442: CKX1 BA 15 #2 GSM28443: CKX1 BA 0 #3 GSM28444: CKX1 BA 15 #3 GSM28445: CKX1 BA 15 #4 204: GSE2268 record: Arabidopsis polysome microarray [Arabidopsis thaliana] Summary: Microarray experiment with polysomal and non-polysomal RNAs extracted under non-stress and mild-dehydration stress. Keywords = translation Keywords = ribosome loading Keywords = polysome Keywords = dehyrdation Samples: 4 GSM38668: NSNP GSM38669: NSPS GSM38670: DSNP GSM38671: DSPS 205: GSE2080 record: Overexpression of miR164b and 172a (vegetative apex) [Arabidopsis thaliana] Summary: RNA was isolated from vegetative apices of 7d-old short-day grown plants. Overexpression of miR164b and miR172a versus control. Samples: 6 GSM37645: 223a GSM37646: 223b GSM37647: 225a GSM37648: 225b GSM37649: 226a GSM37650: 226b 206: GSE2079 record: Overexpression of miR156b and miR164b (floral apex) [Arabidopsis thaliana] Summary: RNA was harvested from floral apices of long-day grown plants. Overexpression of miR156b and 164b versus control. Samples: 6 GSM37639: 220a GSM37640: 220b GSM37641: 221a GSM37642: 221b GSM37643: 222a GSM37644: 222b 207: GSE2078 record: Overexpression of miR159a [Arabidopsis thaliana] Summary: Flowers stage 15: Comparison of miR159a overexpressers to empty-vector control. Samples: 6 GSM37633: 231a GSM37634: 232a GSM37635: 231b GSM37636: 231c GSM37637: 232b GSM37638: 232_c 208: GSE2081 record: Overexpression of miR319a (SD Leaves) [Arabidopsis thaliana] Summary: jaw-D plants grown in SD compared to columbia wt. Samples: 4 GSM37651: 201a GSM37652: 201b GSM37653: 202a GSM37654: 202b 209: GSE2133 record: Effects of anoxia and sucrose on seedling growth [Arabidopsis thaliana] Summary: Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark without added sucrose. Samples were subsequently kept for 6h either [1] under aerobic conditions, [2] under anoxia in absence of sucrose or [3] under anoxia in presence of sucrose. Samples: 6 GSM38613: AIR EXPERIMENT 1 GSM38614: AIR EXPERIMENT 2 GSM38615: ANOXIA EXPERIMENT 1 GSM38616: ANOXIA EXPERIMENT 2 GSM38617: ANOXIA+SUCROSE EXPERIMENT 1 GSM38618: ANOXIA+SUCROSE EXPERIMENT 2 210: GSE1051 record: Seed development in LEAFY COTYLEDON1 mutants [Arabidopsis thaliana] Summary: Analysis of gene expression in Ws-0 lec1 (LEAFY COTYLEDON1) mutant Arabidopsis thaliana. Developmental stages studied includes 24-Hr post-fertilization, globular stage, cotyledon stage, mature green stage, post-mature green stage, and seedlings. Microarray Methods: Total RNA was extracted using the Hot Borate Method [Stones et. al. PNAS vol 98 no 20: 11806-11811 (2001)]. Biotinylated cRNA were prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit (Farmingdale, NY). cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips. The scanned array images were analyzed using Affymetrix Microarray Suite 4.0 (MAS 4.0) with a global scaling intensity set at 500. 2 related Platforms Samples: 30 GSM10445: WT 24-Hr Seed 1 GSM10446: WT 24-Hr Seed 2 GSM10448: WT Cotyledon Stage Seed 1 GSM10449: WT Cotyledon Stage Seed 2 GSM10451: WT Mature Green Seed 1 GSM10453: WT Mature Green Seed 2 GSM10454: WT Post-Mature Green Seed 1 GSM10456: WT Post-Mature Green Seed 2 GSM10457: WT Seedling 1 GSM10458: WT Seedling 2 GSM10477: lec1-1 24-Hr Seed 1 GSM10478: lec1-1 24-Hr Seed 2 GSM10479: lec1-1 Cotyledon Stage Seed 1 GSM10480: lec1-1 Cotyledon Stage Seed 2 GSM10481: lec1-1 Mature Green Seed 1 GSM10482: lec1-1 Mature Green Seed 2 GSM10483: lec1-1 Post-Mature Green Seed 1 GSM10484: lec1-1 Post-Mature Green Seed 2 GSM16996: WT Mid-Maturation Seed 1 (AtGenome1) GSM16997: WT Mid-Maturation Seed 2 (AtGenome1) GSM16998: WT Late-Maturation Seed 1 (AtGenome1) GSM16999: WT Late-Maturation Seed 2 (AtGenome1) GSM17000: lec1 24-Hr Seed 1 (AtGenome1) GSM17001: lec1 24-Hr Seed 2 (AtGenome1) GSM17002: lec1 Mid-Maturation Seed 1 (AtGenome1) GSM17003: lec1 Mid-Maturation Seed 2 (AtGenome1) GSM17007: WT 24-Hr Seed 1 (AtGenome1) GSM17008: WT 24-Hr Seed 2 (AtGenome1) GSM147965: lec1-1 Globular Stage Seed 1 GSM147966: lec1-1 Globular Stage Seed 2 211: GSE680 record: Transcript Profiling of Arabidopsis Plant Life Cycle [Arabidopsis thaliana] Summary: This series contain all stages Arabidopsis plant development. Stages of development includes unfertilized ovule, 24-Hr post-fertilization seed, globular stage seed, cotyledon stage seed, mature green seed, post-mature green seed, post-germination seedling, rosette leaf, root, stem, and floral bud. Keywords = Arabidopsis Keywords = Seed development Keywords = seedling Keywords = germination Keywords = leaf Keywords = root Keywords = stem Keywords = floral bud 2 related Platforms Samples: 30 GSM10441: WT Ovule 1 GSM10442: WT Ovule 2 GSM10445: WT 24-Hr Seed 1 GSM10446: WT 24-Hr Seed 2 GSM10448: WT Cotyledon Stage Seed 1 GSM10449: WT Cotyledon Stage Seed 2 GSM10451: WT Mature Green Seed 1 GSM10453: WT Mature Green Seed 2 GSM10454: WT Post-Mature Green Seed 1 GSM10456: WT Post-Mature Green Seed 2 GSM10457: WT Seedling 1 GSM10458: WT Seedling 2 GSM16996: WT Mid-Maturation Seed 1 (AtGenome1) GSM16997: WT Mid-Maturation Seed 2 (AtGenome1) GSM16998: WT Late-Maturation Seed 1 (AtGenome1) GSM16999: WT Late-Maturation Seed 2 (AtGenome1) GSM17006: WT Ovule 2 (AtGenome1) GSM17007: WT 24-Hr Seed 1 (AtGenome1) GSM17008: WT 24-Hr Seed 2 (AtGenome1) GSM17009: WT Ovule 1 (AtGenome1) GSM27359: WT Floral Bud GSM27360: WT Rosette Leaf GSM27361: WT Root GSM27362: WT Stem GSM27363: lec1-1 Floral Bud GSM27364: lec1-1 Rosette Leaf GSM27365: lec1-1 Root GSM27366: lec1-1 Stem GSM147963: WT Globular Stage Seed 1 GSM147964: WT Globular Stage Seed 2 212: GSE1512 record: flk_vs_wt [Arabidopsis thaliana] Summary: Examination of Columbia-O wildtype and flk mutant tissues under the following conditions: 7 day-old long-day grown, collected 1hr after dawn (exp3: GSM26236- GSM26241); 16 day-old continuous-light-grown (exp2: GSM26230- GSM26235); 16 day-old long-day grown, collected at 16hrs after dawn (exp1: GSM26224- GSM26229). Keywords = Arabidopsis Keywords = flowering Keywords = flk Samples: 18 GSM26224: flk_ath1_exp1_c1 GSM26225: flk_ath1_exp1_c2 GSM26226: flk_ath1_exp1_c3 GSM26227: flk_ath1_exp1_f1 GSM26228: flk_ath1_exp1_f2 GSM26229: flk_ath1_exp1_f3 GSM26230: flk_ath1_exp2_c1 GSM26231: flk_ath1_exp2_c2 GSM26232: flk_ath1_exp2_c3 GSM26233: flk_ath1_exp2_f1 GSM26234: flk_ath1_exp2_f2 GSM26235: flk_ath1_exp2_f3 GSM26236: flk_ath1_exp3_c1 GSM26237: flk_ath1_exp3_c2 GSM26238: flk_ath1_exp3_c3 GSM26239: flk_ath1_exp3_f1 GSM26240: flk_ath1_exp3_f2 GSM26241: flk_ath1_exp3_f3 213: GSE1516 record: Arabidopsis WT and vip mutants (vip5 and vip6) [Arabidopsis thaliana] Summary: Comparison of gene expression profiles of wild-type, vip5 mutant, and vip6 mutant Arabidopsis. Keywords = VIP Samples: 6 GSM26281: WT_1 GSM26282: WT_2 GSM26283: vip5_1 GSM26284: vip5_2 GSM26285: vip6_1 GSM26286: vip6_2 214: GSE862 record: BR effects on WT and yucca seedlings [Arabidopsis thaliana] Summary: Ten-day old light-grown Arabidopsis seedlings were immersed in 1 µM brassinolide in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) or media alone for 2.5 hours Samples: 8 GSM13420: WTmock1 GSM13421: WTmock2 GSM13423: WTBR1 GSM13424: WTBR2 GSM13426: yuccamock1 GSM13427: yuccamock2 GSM13428: yuccaBR1 GSM13429: yuccaBR2 215: GSE863 record: Auxin effects on seedlings [Arabidopsis thaliana] Summary: Five-day old light-grown Arabidopsis seedlings were immersed 10 µM indole-3-acetic acid (auxin) or water Samples: 4 GSM13430: wt(zm)1 GSM13432: wt(zm)2 GSM13433: wt(zm)IAA1 GSM13434: wt(zm)IAA2 216: GSE1491 record: Identification of Inhibitors of Auxin Transcriptional Activation via Chemical Genetics in Arabidopsis [Arabidopsis thaliana] Summary: Approximately 2.5 mg dry Col-0 seedlings were surface sterilized and stratified for 2 days at 4degreesC in liquid media containing 1.5% sucrose (w/v) before being transferred to light with constant shaking at 100 rpm on an orbital shaker. After 7 days, the seedling clusters were subjected to the treatments for 1 hr followed by total RNA isolation using the RNAqueous kit (Ambion). Each treatment was performed in triplicate or quadruplicate. All labeling (Enzo) and hybridization (Affymetrix) procedures were performed as directed by the manufacturers. Raw probe intensities output by the Affymetrix MAS software were processed using the RMA algorithm to obtain an expression measure for each gene on each array. Samples: 21 GSM25858: Negative control - 1 GSM25859: Negative Control - 2 GSM25860: Negative Control - 3 GSM25861: Negative Control - 4 GSM25862: IAA treated - 1 GSM25863: IAA Treated - 2 GSM25864: IAA Treated - 3 GSM25865: IAA Treated - 4 GSM25866: A Treated - 1 GSM25867: A Treated - 2 GSM25868: A treated - 3 GSM25869: A Treated - 4 GSM25870: B Treated - 1 GSM25871: B Treated - 2 GSM25872: B Treated - 3 GSM25873: IAA/A Treated - 1 GSM25874: IAA/A Treated - 2 GSM25875: IAA/A Treated - 3 GSM25876: IAA/B Treated - 1 GSM25877: IAA/B Treated - 2 GSM25878: IAA/B Treated - 3 217: GSE1111 record: Comparison of AG and ATH1 using IAA [Arabidopsis thaliana] Summary: Arabidopsis seedlings (Col-0) were grown in suspension in half-strength MS medium with agitation at ~100 rpm at ~22 C under ~50 microeinsteins m-2s-1 cool white fluorescent continuous illumination as described by (Xiao et al., Plant Physiol. 2002 Dec;130(4):2118-28). Seedlings were treated at 10-12 days by addition of freshly made IAA (0.1 or 1.0uM) to each flask, and harvested after a 1 or 3 hour incubation. Controls were not treated and harvested at 0hr. All tissue harvested. Total RNA was extracted using TRIzol (Invitrogen) as described by the manufacturer and then filtered using QIAGEN RNeasy columns. cDNA was synthesized from total RNA using a Superscript double-stranded cDNA synthesis kit (Invitrogen) and a T7-dT24 primer. cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling kit (Affymetrix p/n 900182) and fragmented by Mg2+ hydrolysis. Samples: 12 GSM18228: Control_1.1 (a) GSM18229: Control_1.2 (a) GSM18290: 0.1uM_IAA_1h_1.1 GSM18291: 0.1uM_IAA_1h_1.2 GSM18294: 0.1uM_IAA_3h_1.1 GSM18295: 0.1uM_IAA_3h_1.2 GSM18325: Control_1.1 (a) AG GSM18326: Control_1.2 (a) AG GSM18327: 0.1uM_IAA_1h_1.1 AG GSM18328: 0.1uM_IAA_1h_1.2 AG GSM18329: 0.1uM_IAA_3h_1.1 AG GSM18330: 0.1uM_IAA_3h_1.2 AG 218: GSE1110 record: Arabidopsis thaliana gene expression in response to IAA challange [Arabidopsis thaliana] Summary: Arabidopsis seedlings (Col-0) were grown in suspension in half-strength MS medium with agitation at ~100 rpm at ~22 C under ~50 microeinsteins m-2s-1 cool white fluorescent continuous illumination as described by (Xiao et al., Plant Physiol. 2002 Dec;130(4):2118-28). Seedlings were treated at 10-12 days by addition of freshly made IAA (0.1 or 1.0uM) to each flask, and harvested after a 1 or 3 hour incubation. Controls were not treated and harvested at 0hr. All tissue harvested. Total RNA was extracted using TRIzol (Invitrogen) as described by the manufacturer and then filtered using QIAGEN RNeasy columns. cDNA was synthesized from total RNA using a Superscript double-stranded cDNA synthesis kit (Invitrogen) and a T7-dT24 primer. cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling kit (Affymetrix p/n 900182) and fragmented by Mg2+ hydrolysis. Samples: 22 GSM18228: Control_1.1 (a) GSM18229: Control_1.2 (a) GSM18230: Control_2.1 GSM18231: Control_2.2 GSM18232: Control_3.1 GSM18233: Control_3.2 GSM18290: 0.1uM_IAA_1h_1.1 GSM18291: 0.1uM_IAA_1h_1.2 GSM18292: 0.1uM_IAA_1h_2.1 GSM18293: 0.1uM_IAA_1h_2.2 GSM18294: 0.1uM_IAA_3h_1.1 GSM18295: 0.1uM_IAA_3h_1.2 GSM18296: 0.1uM_IAA_3h_2.1 GSM18297: 0.1uM_IAA_3h_2.2 GSM18298: 1.0uM_IAA_1h_1.1 GSM18299: 1.0uM_IAA_1h_1.2 GSM18300: 1.0uM_IAA_1h_2.1 GSM18301: 1.0uM_IAA_1h_2.2 GSM18302: 1.0uM_IAA_3h_1.1 GSM18303: 1.0uM_IAA_3h_1.2 GSM18304: 1.0uM_IAA_3h_2.1 GSM18305: 1.0uM_IAA_3h_2.2 219: GSE991 record: YODA lof and gof seedlings [Arabidopsis thaliana] Summary: comparison of 7dpg seedlings of wildtype yda(C24) and N-term deletion of YDA (Ler) for stomatal development comparisons Samples: 14 GSM15661: yda4 GSM15662: yda3 GSM15663: yda2 GSM15664: yda1 GSM15665: ndelYDA1 GSM15666: Ndel-YDA2 GSM15667: NdelYDA3 GSM15668: NdelYDA4 GSM15669: C241 GSM15670: C242 GSM15671: C243 GSM15672: Ler1 GSM15673: Ler2 GSM15674: Ler3 220: GSE641 record: Control vs. 35S:AtRALF1-1 [Arabidopsis thaliana] Summary: This series (two repeats) compares the transcriptional changes caused by the overexpression of the AtRALF1-1 cDNA. AtRALF1-1 is one of the nine Arabidopsis isoforms of the polypeptide hormone RALF (PNAS 98, 12843). Samples: 4 GSM9916: Control 1st repeat GSM9917: Control 2nd repeat GSM9918: 35S:AtRALF1-1 1st repeat GSM9919: 35S:AtRALF1-1 2nd repeat 221: GSE911 record: Identification of LEAFY targets during reproductive transition [Arabidopsis thaliana] Summary: Global analysis of gene expression in 9 day old LEAFY-GR, 35S::LFY or Landsberg erecta seedlings treated with the steroid dexamethasone and/or the protein synthesis inhibitor cycloheximide. Samples: 12 GSM13778: Dexamethasone GSM13779: Dexamethasone plus cycloheximide GSM13780: Cycloheximide GSM13781: Mock GSM13782: Dexamethasone - replicate GSM13783: Dexamethasone plus cycloheximide - replicate GSM13784: Cycloheximide - replicate GSM13785: Mock - replicate GSM13789: 35S::LFY GSM13791: Landsberg erecta GSM13792: 35S::LFY - replicate GSM13793: Landsberg erecta - replicate 222: GSE607 record: Arabidopsis thaliana leaf, stem and flower tissues. [Arabidopsis thaliana] Summary: Analysis of gene expression in Arabidopsis thaliana leaf, stem and flower tissues. Columbia (Col-0) Arabidopsis thaliana plants were grown at a density of 4 plants per 5 inch square pot either in a growth chamber or a green house set to 25*C by day, 20*C by night. Days were set to a 16hr photoperiod with 125 micro mol m-2s-1 fluorescent irradiation. Expanding leaves were harvested 15 days post germination in the middle of the photoperiod (3 replicates). Expanding upper 2" of the stem with siliques and pedicels removed were harvested 29 days post germination in the middle of the photoperiod (4 replicates). Developed flowers and unopened buds were harvested 29 days post germination in the middle of the photoperiod (4 replicates). RNA and Microarray Methods: Total RNA was extracted from the plants using the Trizol method (Invitrogen, Ramonell et al. Samples: 11 GSM9223: Leaf_GC2 GSM9224: Leaf_GH1 GSM9225: Leaf_GH2 GSM9226: STEM_GC7 GSM9227: STEM_GC8 GSM9228: STEM_GH7 GSM9229: STEM_GH8 GSM9230: FLOWER_GC5 GSM9231: FLOWER_GC6 GSM9232: FLOWER_GH5 GSM9233: FLOWER_GH6 223: GSE431 record: pmr4 vs. wild-type (May, 2003) [Arabidopsis thaliana] Summary: There were two genotypes: (1) Columbia-0, wild-type (C) (2) pmr4-1 mutant (P), callose synthase deficient mutant (Vogel and Somerville (2000) Proc. Natl. Acad. Sci., USA 97: 1897). There were two treatments: (1) uninoculated (U) (2) 3 days after inoculation with the powdery mildew pathogen, Erysiphe cichoracearum, race UCSC (I). There were four biological replicates, labeled 1, 2, 3 or 4. Examples of the sample labels are: CU1 = Columbia-0, uninoculated, replicate 1 CI2 = Columbia-0, 3 days after inoculation with powdery mildew, replicate 2 PU3 = pmr4-1, uninoculated, replicate 3 PI4 = pmr4-1, 3 days after inoculation with powdery mildew, replicate 4. In total, there were 16 Affymetrix ATH1 GeneChips (2 genotypes x 2 treatments x 4 biological replicates). Samples: 16 GSM6227: CU4 GSM6544: CU3 GSM6571: CU2 GSM6572: CU1 GSM6573: CI1 GSM6574: CI2 GSM6575: CI3 GSM6576: CI4 GSM6577: PI1 GSM6578: PI2 GSM6579: PI3 GSM6580: PI4 GSM6581: PU1 GSM6582: PU2 GSM6583: PU3 GSM6584: PU4 224: GSE537 record: Seedling ethylene treatment [Arabidopsis thaliana] Summary: Effect of ethylene treatment on wild-type Arabidopsis seedlings (ecotype Col-0). Samples: 8 GSM8467: air1-1 GSM8468: air1-2 GSM8469: air2-1 GSM8470: air2-2 GSM8471: ethylene1-1 GSM8472: ethylene1-2 GSM8473: ethylene2-1 GSM8474: ethylene2-2 225: GSE538 record: Arabidopsis shoot apices dissection [Arabidopsis thaliana] Summary: Comparisin of short day and long day growth conditions for wild-type Arabidopsis seeds (ecotype Col-0). Samples: 4 GSM8475: Col-0-1 GSM8476: Col-0-2 GSM8477: Col-7-1 GSM8478: Col-7-2 226: GSE576 record: Flower development [Arabidopsis thaliana] Summary: Wild type and mutanat Arabiposis plants grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0) Landsberg erecta (Ler) leafy-12 (lfy-12, in Col-0) constans-2 (co-2, in Ler) flowering locus T-2 (ft-2, in Ler) Time points: 0, 3, 5, and 7 days after shift to long days Keywords = flowering Samples: 40 GSM8827: Col_0_1 GSM8828: Col_0_2 GSM8829: Col_3_1 GSM8830: Col_3_2 GSM8831: Col_5_1 GSM8832: Col_5_2 GSM8833: Col_7_1 GSM8834: Col_7_2 GSM8835: lfy-12_0_1 GSM8836: lfy-12_0_2 GSM8837: lfy-12_3_1 GSM8838: lfy-12_3_2 GSM8839: lfy-12_5_1 GSM8840: lfy-12_5_2 GSM8841: lfy-12_7_1 GSM8842: lfy-12_7_2 GSM8843: Ler_0_1 GSM8844: Ler_0_2 GSM8845: Ler_3_1 GSM8846: Ler_3_2 GSM8847: Ler_5_1 GSM8848: Ler_5_2 GSM8849: Ler_7_1 GSM8850: Ler_7_2 GSM8851: co-2_0_1 GSM8852: co-2_0_2 GSM8853: co-2_3_1 GSM8854: co-2_3_2 GSM8855: co-2_5_1 GSM8856: co-2_5_2 GSM8857: co-2_7_1 GSM8858: co-2_7_2 GSM8859: ft-2_0_1 GSM8860: ft-2_0_2 GSM8861: ft-2_3_1 GSM8862: ft-2_3_2 GSM8863: ft-2_5_1 GSM8864: ft-2_5_2 GSM8865: ft-2_7_1 GSM8866: ft-2_7_2 227: GSE518 record: Activation-tagged jaw-d mutant plants [Arabidopsis thaliana] Summary: Analysis of gene expression in activation-tagged jaw-d mutant plants. Total RNA was extracted from the aerial parts of two weeks old jaw-d and control plants. Samples: 4 GSM7754: Control_1 GSM7755: Control_2 GSM7756: jaw_1 GSM7757: jaw_2 |
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