GEO DataSets

(Submitter supplied) Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still far from complete and, due to the low number of ESTs available, evidence for actual transcriptional activity is lacking for most genes. more...

Organism:

Eutrema salsugineum; Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL16263 GPL9020

24 Samples

Download data: TXT

(Submitter supplied) Thellungiella, an Arabidopsis-related halophyte, is an emerging model species for studies designed to elucidate molecular mechanisms of abiotic stress tolerance. Using a cDNA microarray containing 3628 unique sequences derived from previously reported libraries of stress-induced cDNAs of the Yukon ecotype of Thellungiella, we obtained transcript profiles of its response to drought, cold, high salinity and re-watering after drought. more...

Organism:

Thellungiella

Type:

Expression profiling by array

Platform:

GPL2627

24 Samples

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(Submitter supplied) The transcriptional response of T. salsuginea to UV irradiation and AgNO3 was monitored by microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated.

Organism:

Eutrema salsugineum

Type:

Expression profiling by array

Platform:

GPL19319

12 Samples

Download data: TXT

(Submitter supplied) Expression profiling of A. thaliana, A. stelleri, R. islandica, and T. salsuginea under the low-oxygen treatment(0.1% O2/99.9% N2, various time points at 0, 1, 3, 8, 24, 72h) Comparative analysis of transcriptional responses to low-oxygen stress with Arabidopsis and its related species to gain comprehensive insights into low-oxygen responses of the species.

Organism:

Arabidopsis thaliana; Rorippa islandica; Eutrema salsugineum; Arabis stelleri

Type:

Expression profiling by array

Platform:

GPL26403

23 Samples

Download data: TXT

(Submitter supplied) Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.

Organism:

Brassica napus; Brassica rapa; Brassica; Brassica oleracea

Type:

Expression profiling by array

Platform:

GPL8513

16 Samples

Download data: TXT

(Submitter supplied) Background: The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. more...

Organism:

Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17514

10 Samples

Download data: TXT

(Submitter supplied) Background: Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm. more...

Organism:

Thellungiella

Type:

Expression profiling by array

Platform:

GPL2627

12 Samples

Download data: TXT

(Submitter supplied) This is a song bird (Junco hyemalis) whole-genome expression array in HD2 12x135K format manufactured by Roche NimbleGen. DESIGN_ID : 537583 native array description file : 100702_Jhye_JL_exp.ndf native array description file : 100702_Jhye_JL_exp.txt Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, Buechlein A, Podicheti R, Choi JH, Lai Z, Mockatis K, Colbourne J, Tang H, Ketterson ED. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. more...

Organism:

Junco hyemalis

1 Series

48 Samples

Download data: NDF, TXT

(Submitter supplied) We have developed a method based on 454 sequencing of 3’ cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This “virtual transcriptome” provides extensive coverage depth, and can be used for the set up of a comprehensive microarray based expression analysis. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platforms:

GPL8025 GPL8024

3 Samples

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(Submitter supplied) Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12) Protocol: A.thaliana genes were predicted with Eugene software (Foissac S. et al., Nucleic Acids Res., 2003) and gene-specific sequence tags were automatically designed (Thareau et al. Bioinformatics, 2003 Nov 22). Two rounds of PCR were performed and PCR products were finally purified and dissolved in 50% DMSO in TE at concentrations ranging between 50-200ng/ul and re-arrayed in 1536 microtiter plates. more...

Organism:

Arabidopsis thaliana

95 Series

1171 Samples

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(Submitter supplied) The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. more...

Organism:

Enchytraeus crypticus

Type:

Expression profiling by array

Platform:

GPL17851

8 Samples

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(Submitter supplied) Samples in this study probe the gene expression kinetics in human CCR6+ Th17 memory T cells activated under Th17 condition. Human CCR6+ Th17 memory T cells were purified from PBMC and gene expression was studied over a time course of 3 days after activation under Th17 condition. RNA from these samples was also profiled using RNA-Seq to compare different transcriptome profiling technologies.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

12 Samples

Download data: CEL

(Submitter supplied) Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profil-ing and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. more...

Organism:

Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20016

2 Samples

Download data: XLSX

(Submitter supplied) mRNA degradation provides a powerful means for controlling gene expression during growth, development, and many physiological transitions in plants and other systems. Rates of decay help define the steady state levels to which transcripts accumulate in the cytoplasm and determine the speed with which these levels change in response to the appropriate signals. When fast responses are to be achieved, rapid decay of mRNAs is necessary. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL2823

6 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana; Hirschfeldia incana

Type:

Expression profiling by array

Platform:

GPL12621

12 Samples

Download data: TXT

(Submitter supplied) Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 µM Pb(NO3)2.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

6 Samples

Download data: TXT

(Submitter supplied) Experiments were achieved on Hirschfeldia incana, a Brassicaceae collected from metalliferous mine spoils as a Pb accumulator plant. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old H. incana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 100 µM Pb(NO3)2.

Organism:

Hirschfeldia incana; Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

6 Samples

Download data: TXT

(Submitter supplied) To gain plant compactness, producers use plant growth regulators (PGRs), in particular growth retardants during culture. However, due to their negative environmental impacts, growth retardants are progressively withdrawn from the market. Alternative, eco-friendly methods such as mechanical stimulation (MS), which mimics the effect imposed on plants by the wind, result in reduced stem elongation, increased stem diameter and increased branching, all of which contribute to plant compactness. more...

Organism:

Hydrangea macrophylla

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33625

27 Samples

Download data: FASTA, TXT

(Submitter supplied) A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. more...

Organism:

soil metagenome

Type:

Expression profiling by array

Platform:

GPL13295

8 Samples

Download data: TXT