GEO DataSets

(Submitter supplied) Background The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche’s 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11675

4 Samples

Download data

(Submitter supplied) Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. more...

Organism:

Saccharum hybrid cultivar SP70-1143

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16317

4 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) Purpose: To identify Fusarium wilt and salt-responsive miRNAs at genome wide level in Chickpea. Results: A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume specific miRNAs, miR5213, miR5232, miR2111 and miR2118 were found in all the libraries. The Poly (A) tailing assay based qRT-PCR was used to validate eleven conserved and five novel miRNAs. more...

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16348

3 Samples

Download data: TXT

(Submitter supplied) In this study, we sequenced small RNA content from seven major tissues/organs employing Illumina technology. More than 154 million reads were generated using Illumina high-throughput sequencing GAII platform, which represented more than 20 million distinct small RNA sequences. After pre-processing, several conserved and novel miRNAs were identified in chickpea. Further, the putative targets of chickpea miRNAs were identified and their functional categorization was analyzed. more...

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16348

7 Samples

Download data: FA

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

Organism:

Lathyrus sativus; Cicer arietinum; Lens culinaris

Type:

Expression profiling by array

Platform:

GPL3649

32 Samples

Download data: TXT

(Submitter supplied) ‘Pulsechip’, a boutique cDNA microarray, generated from a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, was employed to generate an expression profile of chickpea accessions tolerant and susceptible to high-salinity stress. Two groups of a tolerant and susceptible accession were challenged with high-salinity stress. more...

Organism:

Lens culinaris; Cicer arietinum; Lathyrus sativus

Type:

Expression profiling by array

Platform:

GPL3649

16 Samples

Download data: TXT

(Submitter supplied) ‘Pulsechip’, a boutique cDNA microarray, generated from a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, was employed to generate an expression profile of chickpea accessions tolerant and susceptible to cold stress. Two groups of a tolerant and susceptible accession were challenged with cold stress. The experiments were performed in three biological replications. more...

Organism:

Lens culinaris; Cicer arietinum; Lathyrus sativus

Type:

Expression profiling by array

Platform:

GPL3649

8 Samples

Download data: TXT

(Submitter supplied) ‘Pulsechip’, a boutique cDNA microarray, generated from a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, was employed to generate an expression profile of chickpea accessions tolerant and susceptible to drought stress. Two groups of a tolerant and susceptible accession were challenged with drought stress. The experiments were performed in three biological replications. more...

Organism:

Lens culinaris; Cicer arietinum; Lathyrus sativus

Type:

Expression profiling by array

Platform:

GPL3649

8 Samples

Download data: TXT

(Submitter supplied) Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. more...

Organism:

Petunia x hybrida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21338

32 Samples

Download data: CSV, FA, TXT

(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) 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) In this study, the root tissues from the salt tolerant genotype (JG 11) and the salt sensitive genotype (ICCV 2) were analyzed using RNA sequencing to identify genes/pathways associated with salt tolerance/sensitivity in the both genotypes.

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22390

24 Samples

Download data: TXT

(Submitter supplied) Sunflower is an important source of vegetable oil worlwide. A differential organ-specific sunflower ESTs was previously generated by a subtractive hybridization method, including a considerable number of abiotic stress associated sequences. The objective of this work is to analyze the sunflower gene expression of previously identified candidate genes under a comprehensive microarray analysis of the leaf transcriptoma under cold and salinity stresses, considering the impacts of these abiotic stresses on sunflower yield in many productive areas. more...

Organism:

Helianthus annuus

Type:

Expression profiling by array

Platform:

GPL4366

18 Samples

Download data

(Submitter supplied) Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. more...

Organism:

Salicornia europaea

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19315

6 Samples

Download data: FA

(Submitter supplied) Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C. Plantlets with 4–5 leaves were chosen for use in stress treatments. Experiments were conducted with treatment groups: The control (C, without any chemical treatment), TM (treated with 5 μg mL-1 tunicamycin (TM)) and salt (treated with 400 mM NaCl). more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL1320

24 Samples

Download data: CEL

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

Organism:

Olea europaea

Type:

Expression profiling by array

Platform:

GPL15288

76 Samples

Download data: GPR

(Submitter supplied) A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. more...

Organism:

Olea europaea

Type:

Expression profiling by array

Platform:

GPL15288

40 Samples

Download data: GPR

(Submitter supplied) A transcriptomics approach was used as a tool to unravel gene regulatory network underlying salinity response in a salt-tolerant olive cultivar (cv. Kalamon) by simulating as much as possible olive growing conditions in the field. A 135 day long salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. more...

Organism:

Olea europaea

Type:

Expression profiling by array

Platform:

GPL15288

36 Samples

Download data: GPR