GEO DataSets

(Submitter supplied) We generated the global transcriptome profile of the two chickpea genotypes under control and drought conditions. Approximately 12 million high-quality reads were obtained for each cultivar and different conditions using the Illumina platform. Reference-based assembly was generated for each cultivar and condition. Differentially expressed genes were identified between drought and control conditions for each cultivar.

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31174

8 Samples

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(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 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) Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32287

4 Samples

Download data: CSV

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics in different tissues/organs/developmental stage in chickpea. We generated about ~31-95 million reads from each of 94 libraries representing 32 different tissues/organs using Illumina platform. We generated a hybrid assembly of these data along with PacBio data to produce full-length transcriptome assembly. We mapped the reads to the transcriptome assembly for estimation of the abundance of coding and long non-coding transcripts in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

32 Samples

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(Submitter supplied) As a broad group, hemibiotrophic pathogens cause significant losses within agriculture threatening the sustainability of food systems globally. The complex manner in which these microbes colonize their hosts, including an initial biotrophic phase of colonization followed by a biotrophic-to-necrotrophic switch (BNS) phase and ending with a necrotrophic mode of nutritional acquisition, renders their management more complex than pathogens which display a single nutritional strategy. more...

Organism:

Cicer arietinum; Phytophthora medicaginis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30539

16 Samples

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(Submitter supplied) In this study, to obtain a clear picture of drought mechanism involved in two distinctive chickpea genotype, the aim was to identify the DNA methylation patterns which potentially regulate drought tolerance/sensitivity of these selected genotypes. The leaf tissues from the shoot apical meristem from drought sensitive and drought tolerant genotypes were used for RRBS (Reduced representation bisulphite sequencing) under drought stress. more...

Organism:

Cicer arietinum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26370

12 Samples

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(Submitter supplied) The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29457

36 Samples

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(Submitter supplied) In this study, we sequenced small RNAs at seven successive stages of seed development and leaf tissue in a small-seeded chickpea cultivar (Himchana 1) 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 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, the leaf tissue from shoots apical meristem stage of drought tolerant (ICC8261) and drought sensitive (ICC283) genotypes were analyzed using RNA sequencing to identify genes/pathways associated with drought tolerance/sensitivity in the both genotypes. It was observed that genes related to ethylene response, MYB-related protein, xyloglucan endotransglycosylase, alkane hydroxylase MAH-like, BON-1 associated, peroxidase 3, cysteine rich and transmembrane domain, vignain and mitochondrial uncoupling were specifically up-regulated in the tolerant genotype whereas, same genes were down-regulated in sensitive genotype.

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

12 Samples

Download data: CSV, TXT

(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:

GPL23991 GPL20619

5 Samples

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(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 arietinum; Cicer reticulatum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23991 GPL20619

5 Samples

Download data: CSV, ZIP

(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

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(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) Purpose: Molecular analysis of chickpea-Foc interaction; Methods: Four LongSAGE libraries of wilt-resistant and wilt-susceptible chickpea cultivars prepared after Foc inoculation and sequenced using Ion Torrent PGM. Results: Transcriptome analyses revealed expression of several plant defense and pathogen virulence genes with their peculier expression patterns in wilt-resistant and wilt-susceptible chickpea cultivars. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22390

4 Samples

Download data: TXT