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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Arabidopsis under simualted acid rain treatments

ABSTRACT: Acid rain, as a worldwide environmental issue, can cause serious damage to plants. In this study, we provided the first case study on the systematic responses of arabidopsis (Arabidopsis thaliana (L.) Heynh.) to simulated acid rain (SiAR) by transcriptome approach. In this dataset, we include the expression data obtained from Arabidopsis with simulated acid rain treatments for 68 hr, and contrasting with control group in the same time. Totally, 439 differetal expression genes were obtained in our stduy. Form them, 13 genes which dramatically changed their expression were found related to S metabolism. 6 Total samples were analyzed. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). Preparation of labeled target cRNA was carried out following the technical manual of Arabidopsis Genome GeneChip array (Affymetrix). Double-stranded cDNA was synthesized from 5 M-NM-

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Tingwu Liu

PROVIDER: E-GEOD-52487 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from Arabidopsis under simualted acid rain treatments

Project description:Acid rain, as a worldwide environmental issue, can cause serious damage to plants. In this study, we provided the first case study on the systematic responses of arabidopsis (Arabidopsis thaliana (L.) Heynh.) to simulated acid rain (SiAR) by transcriptome approach. In this dataset, we include the expression data obtained from Arabidopsis with simulated acid rain treatments for 68 hr, and contrasting with control group in the same time. Totally, 439 differetal expression genes were obtained in our stduy. Form them, 13 genes which dramatically changed their expression were found related to S metabolism.

2013-11-20 | GSE52487 | GEO

Transcription profiling of Arabidopsis leaf samples treated with salicylic acid

Project description: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 involved in systemic acquired resistance in Arabidopsis. Experiment Overall Design: 3 mock-treated and 3 SA-treated biological replicates were analyzed (one array each)

2007-10-04 | E-GEOD-3984 | biostudies-arrayexpress

Identification of new and unpredicted full length Arabidopsis genes

Project description:Examination of cRNA from Arabidopsis flowers, roots and suspension cell culture using custom high-density Affymetrix genome tiling arrays in order to identify new and unpredicted genes. Keywords: other

2003-10-30 | GSE601 | GEO

Seed development in LEAFY COTYLEDON1 mutants

Project description: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. Keywords: other

2005-01-01 | GSE1051 | GEO

Identification of new full length Arabidopsis genes - pilot arrays

Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at 4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays. Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions. Keywords: other

2003-10-30 | GSE604 | GEO

Transcriptome changes triggered by Hyaloperonospora parasitica arabidopsis Noco2 in WT and wrky72 mutants at 96 hpt

Project description:Functional characterization of AtWRKY72 using Arabidopsis T-DNA insertion lines showed that this gene is important for basal defense to root-knot nematode (RKN) and Hyaloperonospora parasitica arabidopsis (Hpa), but not several tested R gene-mediated defenses.To profile transcriptional reprogramming associated with AtWRKY72-dependent basal defense we used Affymetrix ATH1 GeneChips representing ~24,000 Arabidopsis genes. Three independent biological replicates were performed with Col-0, wrky72-1 and wrky72-2 plants at 96 hpt with HpaNoco2 or mock treatment. Using a false discovery rate of less than 0.05 we identified for each of these three lines genes that showed significant transcriptional changes in response to HpaNoco2 compared to the mock-treated controls. Identification of downstream targets of WRKY72 in Arabidopsis by this microarray suggests that WRKY72 uses a unique signaling pathway that involves AP2/ERF TFs independent of the ethylene signaling pathway. We intended to identify Arabidopsis genes that are regulated in WRKY72-dependent manner in response to Hyaloperonospora parasitica arabidopsis (Hpa) at 96 hpt. For this, we used Col-0 and two wrky72 mutant lines and compared the differentially expressed genes with the hypothesis ‘genes that are specifically regulated in Col-0 but not in wrky72 mutants are WRKY72-dependent genes’.

2010-08-09 | E-GEOD-18329 | biostudies-arrayexpress

Transcription profiling of Arabidopsis thaliana seedlings treated with synthetic defense elicitors 3,5-Dichloroanthranilic acid (DCA) and 2,6-Dichloroisonicotinic acid (INA)

Project description:DCA (3,5-Dichloroanthranilic acid) is a newly identified synthetic defense elicitor. To perform a comparative analysis of defense responses triggered by DCA and the structurally related defense inducer INA (2,6-Dichloroisonicotinic acid) Affymetrix chip experiments were performed with Arabidopsis thaliana seedlings treated with one of these two compounds. Experiment Overall Design: Arabidopsis thaliana plants (accession Col-0) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s). Wild type Col-0 plants and the npr1-3 mutant were used in this study. Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment. Final DMSO concentrations never exceeded 0.002%. Mock treatments were application of 0.002% DMSO in water. For harvesting the aerial plant parts were shock-frozen in liquid nitrogen. Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturerâ??s instructions. RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturerâ??s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility. Three independent biological replicates were performed for each treatment.

2009-03-28 | E-GEOD-13833 | biostudies-arrayexpress

Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance

Project description:Although evidence accumulates on the role of plant peptides in the response to external conditions, the number of peptide-encoding genes in the genome is still underestimated. In order to identify novel oxidative stress-induced peptides in Arabidopsis thaliana a tiling array analysis (GeneChipM-BM-. Arabidopsis Tiling 1.0R Arrays ) was performed on mRNA extracted from leaves treated with paraquat (PQ), an reactive oxygen species inducer and water (control), resulting in the identification of 92,844 and 86,272 transcriptionally active regions (TARs), respectively. Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a treshold, based on positive controls. Next, groups of 4-13 successive ON probes were combined into short TARs and a selection was made of TARs having an average signal intensity at least 2.6-fold higher after PQ treatment compared to the control treatment, resulting in 176 TARS induced by PQ. paraquat treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)

2013-08-31 | E-GEOD-49001 | biostudies-arrayexpress

Transcription profiling of Arabidopsis treated with silwet for varying time and high throughout haplotyping and single feature polymorphism markers in Arabidopsis

Project description: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 (SA) and jasmonic acid (JA), 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. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We assessed Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) for natural variation in the response to SA. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 4, 28, or 52 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for Bay-0 and Sha. These GeneChips were used to generate genetic markers which allowed the development of high-density haplotype maps of a Bay-0 x Sha RIL population.

2007-01-01 | E-TABM-61 | biostudies-arrayexpress

Identification of ORS1 target genes using inducible overexpression system

Project description:The aim was to identify early target genes of the senescence-associated transcription factor: ORS1. For this purpose we used DEX-inducible system and studied the expression profile 5h after treatment using Affymetrix microarray. Keywords: genetic modification Arabidopsis 46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression) were sprayed with 30µM DEX for 5h. As control mock (0.05% ethanol) treated ORS1-inducible over-expression plants were used. Whole rosettes were harvested 5h after induction and used for expression profiling using Affymetrix near-full genome ATH1 arrays. Experiment performed in two biological replications.

2010-12-01 | E-GEOD-22836 | biostudies-arrayexpress

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