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AtTOME: Gene Expression Atlas Data Sources ( Feb. 8, 2008 ) |
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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 GSM13 |