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| Status |
Public on Feb 15, 2023 |
| Title |
Gene expression profiling during salinity stress response in chickpea (RNA-Seq) |
| Organism |
Cicer arietinum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Total RNA was extracted and cDNA libraries were prepared from salinity sensitive (ICCV2) and salinity tolerant (JG62) genotypes under salinity stress and control conditions from 17 day old seedlings. RNA-sequencing was performed on Illumina platform to generate 49 bp single-end reads. Pre-processing was performed using NGS QC Toolkit to remove adapters and low-quality reads below 20 Phred score. Filtered high-quality reads were mapped on the Kabuli chickpea genome using TopHat2 (v2.1.1). To analyze gene expression, reference-guided assembly was generated using Cufflinks (v2.2.1) and differential expression of genes was determined by Cuffdiff (v2.2.1).
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| Contributor(s) |
Gupta K, Garg R |
| Citation(s) |
36768187 |
| Submission date |
May 24, 2022 |
| Last update date |
Feb 15, 2023 |
| Contact name |
Rohini Garg |
| E-mail(s) |
rohini.garg@snu.edu.in
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| Phone |
09560056446
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| Organization name |
Shiv Nadar University
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| Street address |
Shiv Nadar University, NH - 91, Tehsil Dadri
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| City |
Gautam Buddha Nagar |
| State/province |
UP |
| ZIP/Postal code |
201314 |
| Country |
India |
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| Platforms (1) |
| GPL32287 |
Illumina NextSeq 500 (Cicer arietinum) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE204730 |
Salinity stress response in chickpea |
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| Relations |
| BioProject |
PRJNA842022 |
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