GEO DataSets

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9316

7 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13160

8 Samples

Download data

(Submitter supplied) Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. more...

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

4 Samples

Download data: XLSX

(Submitter supplied) Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

4 Samples

Download data: XLSX

(Submitter supplied) In this study, we aim to present the complete transcriptome of Asian wild rice, Porteresia. We generated about 375 million high-quality reads for five different conditions (ranging from 65 to 90 million reads for each condition) using Illumina high-throughput sequencing GAII platform. We mapped the reads to Porteresia transcripts for estimation of their transcriptional activity in different tissue samples. more...

Organism:

Oryza coarctata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16758

5 Samples

Download data: TXT

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

8 Samples

Download data: TXT

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during drought stress in different chickpea genotypes. We generated about 800 million high-quality reads from 14 libraries (control and stress samples for two chickpea genotypes for drought stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

8 Samples

Download data: TXT

(Submitter supplied) To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: TXT

(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) Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. more...

Organism:

Oryza rufipogon

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15800

4 Samples

Download data: TXT

(Submitter supplied) With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. more...

Organism:

Medicago sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22234

27 Samples

Download data: DIFF, FASTA

(Submitter supplied) Changes in the gene expression during exposure to salinity stress were compared among nodal roots, S-type lateral roots, and L-type lateral roots.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: FPKM_TRACKING, TXT, XLSX

(Submitter supplied) Changes in the gene expression during exposure to salinity stress were compared among nodal roots, S-type lateral roots, and L-type lateral roots.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Traditional rice varieties found in India have many desirable characteristics. Amongst them, their differential responses to abiotic and biotic stresses are of great agricultural importance. Drought or osmotic stress is one of the major abiotic stresses afflicting crop plants in India. Indigenous varieties like Dagad deshi have been found to be drought resistant and, thereby, are being studied in great detail by plant breeders and biotechnologists alike. more...

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

18 Samples

Download data: CEL

(Submitter supplied) Purpose: The goals of this study are to compare differentially expressed transcripts in seedlings of watermelon during salt stress using transcriptome profiling (RNA-seq)

Organism:

Citrullus lanatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28123

6 Samples

Download data: XLSX

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

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

16 Samples

Download data: TXT

(Submitter supplied) Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: TXT

(Submitter supplied) To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

10 Samples

Download data: TXT

(Submitter supplied) Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expression of alkali-responsive genes in rice has not previously investigated. In this study, the transcriptomic data were compared between an alkaline-tolerant [WD20342 (WD)] and an alkaline-sensitive [Caidao (CD)] rice cultivar under control and alkaline stress conditions. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

12 Samples

Download data: TXT

(Submitter supplied) Purpose: Brassica. juncea is vulnerable to abiotic stresses at specific stages in its life cycle. However, till date no attempts have been made to elucidate the genome-wide changes in the transcriptome of B. juncea subjected to either high temperature or drought stress. Hence, to gain global insights into genes, transcription factors and kinases regulated by these stresses and to provide basic information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de novo assembly to discover B. more...

Organism:

Brassica juncea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16439

6 Samples

Download data: BED, DIFF, FA, FPKM_TRACKING, TXT