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| Status |
Public on Jul 08, 2016 |
| Title |
Transcriptional response to salinity stress in chickpea |
| Organism |
Cicer arietinum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype.
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| Overall design |
We collected roots of chickpea genotypes from vegetative and reproductive stage plants subjected to control (water) and salinity (irrigated with 80 mM NaCl solution) stress. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stress conditions were identified.
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| Contributor(s) |
Garg R, Jain M |
| Citation(s) |
26759178 |
| Submission date |
Jun 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mukesh Jain |
| Phone |
91-11-26704686
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| Organization name |
Jawaharlal Nehru University
|
| Street address |
New Mehrauli Road
|
| City |
New Delhi |
| State/province |
New Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
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| Platforms (1) |
| GPL20619 |
Illumina HiSeq 2000 (Cicer arietinum) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA288473 |
| SRA |
SRP059951 |
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