GEO DataSets

(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) 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:

Arabidopsis thaliana; Eutrema salsugineum

Type:

Expression profiling by array

Platforms:

GPL16263 GPL9020

24 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:

Arabis stelleri; Eutrema salsugineum; Arabidopsis thaliana; Rorippa islandica

Type:

Expression profiling by array

Platform:

GPL26403

23 Samples

Download data: TXT

(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) 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) This study utilized next generation sequencing technology (RNA-Seq) to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) to elucidate those genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13779

24 Samples

Download data: CSV

(Submitter supplied) A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28757

6 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) Transformation of Glycine max with seed-targeted expression vectors via Agrobacterium causes measurable unscripted gene expression changes in the seed transcriptome

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

36 Samples

Download data: GTF

(Submitter supplied) Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. more...

Organism:

Cucurbita moschata; Citrullus lanatus; Cucurbita pepo; Lagenaria siceraria

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

152 Samples

Download data: TXT

(Submitter supplied) Time-course transcriptional profiling of rice leaf in the field in 2009. This experiment was performed to validate the results of field transcriptomic modeling. Using 461 field transcriptome data obtained in 2008 (GSE36040; GSE36042; GSE36043; GSE36044; GSE18685) and the corresponding meteorologicla dara, we perfomred statistical modeling of transcriptome.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

108 Samples

Download data: TXT

(Submitter supplied) Time-course transcriptional profiling of rice leaf of the temperature shift experiment in a growth chamber. This experiment was performed to validate the results of field transcriptomic modeling.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

16 Samples

Download data: TXT

(Submitter supplied) We have characterized the transcriptional response in Maize under limiting and sufficient nitrogen conditions, and have identified a set of genes whose expression profiles can quantitatively assess the response of plants to those conditions.

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL14616

90 Samples

Download data: CEL

(Submitter supplied) Purpose: Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. more...

Organism:

Eucalyptus nitens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18542

12 Samples

Download data: TXT

(Submitter supplied) The extent to which plants can enhance human life support on other worlds depends on the ability of plants to thrive in extraterrestrial environments using in situ resources. Using samples from Apollo 11, 12 and 17, we show that the terrestrial plant Arabidopsis thaliana germinates and grows in diverse lunar regoliths. However, our results show that growth is challenging; the lunar regolith plants were slow to develop, expressed genes indicative of ionic stresses, and many showed severe stress morphologies. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

20 Samples

Download data: XLSX

(Submitter supplied) Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL21785

728 Samples

Download data: TSV, TXT

(Submitter supplied) Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. more...

Organism:

Pectobacterium atrosepticum SCRI1043

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20147

2 Samples

Download data: TAB, XLSX

(Submitter supplied) We extended the investigation of nuclear transcript changes under drought to an overarching characterization of the post(transcriptome), including alternative splicing of nuclear transcripts, accumulation of organellar (chloroplast and mitochondrion) transcripts, editing and splicing of organellar transcripts, and furthermore, accumulation of transposable elements. To this end, long non-coding (lncRNA-Seq) instead of mRNA-Seq was applied, because the lncRNA-Seq workflow employs library preparation after ribosomal RNA depletion instead of library preparation of enriched mRNAs (mRNA-Seq).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

29 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL198 GPL19580

12 Samples

Download data: CEL