GEO DataSets

(Submitter supplied) In this study, we performed transcriptomic analysis salinity stress response in salinity sensitive and tolerant genotypes of chickpea using Illumina platform. A total of 87 million reads in RNA-sequencing data were generated in all the samples. Mapping of the reads to the Kabuli genome was performed using tophat (v2.1.1). Differentially expressed genes were identified using cufflilnks-cuffdiff (2.2.1) pipeline.

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32287

8 Samples

Download data: TXT

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

Organism:

Cicer arietinum

Type:

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

Platform:

GPL32287

20 Samples

Download data: FA, TXT

(Submitter supplied) Bisulphite sequencing of salinity sensitive and salinity tolerant chickpea genotypes during salinity stress response using Illumina platform has been performed. At least 195 million reads in bisulphite sequencing were generated in each sample. Methylated cytosines in each sample were identified for their genomic location and sequence context.

Organism:

Cicer arietinum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL32287

8 Samples

Download data: TXT

(Submitter supplied) In this study, we have identified small RNA during salinity stress response in chickpea. Small RNA library was prepared and sequencing was performed using Illumina platform. A total of 79 million reads were generated. These reads were mapped to the chickpea genome using Bowtie.

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL32287

4 Samples

Download data: FA

(Submitter supplied) In this study, we have elucidated the DNA methylation patterns in different organs of a cultivated chickpea genotype ICC 4958 (leaf, root, flower and young pod) and leaf of wild chickpea PI 489777 using bisulphite sequencing. Approximately 108 million read pairs were analyzed per sample. The extent of methylation along-with the context and genomic location of methylated Cs was identified. Further processing was performed to identify the differentially methylated regions among samples with leaves of ICC 4958 as the reference sample. more...

Organism:

Cicer arietinum; Cicer reticulatum

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL20619 GPL23991

5 Samples

Download data: TXT

(Submitter supplied) We report small RNA data from the leaves of wild chickpea PI 489777. Small RNA library was prepared and sequencing was performed using Illumina platform. A total of 23 million reads were generated, which represented 0.95 million unique reads. These were mapped to the chickpea genome using Bowtie to obtain the non-redundant set of unique small RNA sequences.

Organism:

Cicer reticulatum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23991

1 Sample

Download data: FASTA

(Submitter supplied) In this study, global transcriptome profiling was performed for different organs of ICC 4958 (leaves, roots, flowers and young pod) and leaves of wild chickpea, PI 489777. More than 50 million high-quality reads were obtained from each sample using Illumina platform. A consensus reference-guided assembly was generated for the transcriptome data from all samples and gene expression was analysed.

Organism:

Cicer reticulatum; Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23991 GPL20619

5 Samples

Download data: CSV, ZIP

(Submitter supplied) In this study, we performed bisulphite of two stages of seed development in a small-seeded chickpea cultivar (Himchana 1) using Illumina platform. Paired-end reads were generated from 5 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.

Organism:

Cicer arietinum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20619

5 Samples

Download data: TXT

(Submitter supplied) In this study, we performed bisulphite of five stages of seed development in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. Paired-end reads were generated from 11 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.

Organism:

Cicer arietinum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20619

11 Samples

Download data: TXT

(Submitter supplied) In this study, we sequenced small RNAs at seven successive stages of seed development and leaf tissue in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. More than 500 million reads were generated in all the samples combined together with an average of 34 million reads in each sample. Data obtained in FASTQ files were pre-processed and unique reads representing small RNAs were identified at different stages of seed development.

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20619

15 Samples

Download data: FA

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during seed development in a small-seeded chickpea (genotype Himchana 1). We generated about 1.5 billion high-quality reads from 24 libraries (leaf and seven seed developmental stages in three biological replicates) 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

24 Samples

Download data: TXT

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during seed development in a large-seeded chickpea (genotype JGK3). We generated about 1.5 billion high-quality reads from 24 libraries (leaf and seven seed developmental stages in three biological replicates) 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

24 Samples

Download data: TXT

(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) 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

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(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:

Cicer arietinum; Lens culinaris; 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:

Cicer arietinum; Lathyrus sativus; Lens culinaris

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:

Cicer arietinum; Lens culinaris; Lathyrus sativus

Type:

Expression profiling by array

Platform:

GPL3649

8 Samples

Download data: TXT

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

Organism:

Glycine max

Type:

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

Platform:

GPL15087

12 Samples

Download data: TXT