GEO DataSets

(Submitter supplied) We sought to investigate the scope of transcriptome analyses of peppers subjected to four major environment stresses (heat, cold, drought, and salinity). For this, at the six-true-leaf stage, plants were subjected to a temperature of 10°C or 40°C to mimic cold or heat stress, respectively. For salinity stress, plants were treated with 50 mL of a 400 mM NaCl solution; for osmotic stress, the peppers were treated with 50 mL of 400 mM mannitol. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

78 Samples

Download data: TXT

(Submitter supplied) We sought to investigate the scope of transcriptome analyses of peppers subjected to four major phytohormones. For this, At the 6-true-leaf stage, pepper plants were sprayed at underside of leaves with 5 mM sodium salicylate (SA), 100 μM methyl jasmonate (JA), 5 mM ethephone (ET), 100 μM (±)-ABA, or distilled water (mock). For RNA-seq library construction, the third or fourth leaves from four plants were harvested per replicate at 0, 1, 3, 6, 12, and 24 h after treatment. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

78 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

(Submitter supplied) Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29996

4 Samples

Download data: FA, GFF3, TSV

(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) We take the one year old plant for chilling stress (4°C, 10h) and controls.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves. We used microarrays to detail the global programme of gene expression during chilling stress (4°C, 10h).

Organism:

Populus simonii; Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

4 Samples

Download data: CEL, CHP

(Submitter supplied) We take the one year old plant for 100 mMol/L NaCl treatments 24 hours and controls. Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves. We used microarrays to detail the global programme of gene expression during NaCl treatments.

Organism:

Populus sp.; Populus simonii

Type:

Expression profiling by array

Platform:

GPL4359

6 Samples

Download data: CEL, CHP

(Submitter supplied) We take one-year-old plants for high-temperature treatments and controls. We used the Affymetrix Poplar GeneChip to decrypt the gene functions and mechanisms in Populus simonii leaves.

Organism:

Populus simonii; Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

4 Samples

Download data: CEL, CHP

(Submitter supplied) We take one-year-old plants for short-term water deficit treatments and controls. We use the Affymetrix Poplar GeneChip to decrypt the gene functions and mechanisms in Populus simonii leaves and detail the global program of gene expression during water deficit treatments.

Organism:

Populus simonii; Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

4 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose:Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16485

12 Samples

Download data

(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) Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of sa;t-down shock on Halothece transcriptomes were examined using RNA sequencing.

Organism:

Halothece sp. PCC 7418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32361

2 Samples

Download data: XLSX

(Submitter supplied) Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of five different stimuli on Halothece transcriptomes were examined using RNA sequencing. In response to diverse stresses, there were both common and stress-specific transcriptional responses.

Organism:

Halothece sp. PCC 7418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32361

7 Samples

Download data: TXT

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

Organism:

Capsicum annuum; Capsicum chinense; Capsicum annuum var. glabriusculum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16780 GPL16781 GPL16195

38 Samples

Download data

(Submitter supplied) To facilitate the functional annotation of the pepper genome, analysis of miRNAs was performed for the sequenced data from five small RNA libraries described above, representing five different tissues. Starting with a set of 5,436 plant mature miRNA sequences available in miRBase, we annotated with high confidence 176 pepper miRNAs from 64 families, of which 30 families are computationally predicted to target TFs, suggesting important roles of these miRNA families in post-transcriptional gene regulation and transcription networks consistent with previous findings.

Organism:

Capsicum annuum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16195

5 Samples

Download data: GFF

(Submitter supplied) To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences.

Organism:

Capsicum chinense; Capsicum annuum; Capsicum annuum var. glabriusculum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16195 GPL16780 GPL16781

33 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) Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29650

179 Samples

Download data: CSV, FA, GTF