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| Status |
Public on Dec 31, 2017 |
| Title |
Transcriptome dynamics during seed development in chickpea (JGK3) |
| 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 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. The transcriptome dynamics was studied by differential gene expression analyses between different samples/stages.
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| Overall design |
We collected leaves from the field-grown chickpea plants during mid maturation stage of seed development. Seven different stages of seeds (whole seed) representing the major events occurring within the seed, were collected from the field-grown plants. The tissues were collected in at least three biological replicates. 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 samples to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stages of seed development were identified.
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| Contributor(s) |
Jain M, Singh V, Kumar V, Garg R |
| Citation(s) |
32620865 |
| Submission date |
Mar 30, 2016 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Mukesh Jain |
| Phone |
91-11-26704686
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| Organization name |
Jawaharlal Nehru University
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| Street address |
New Mehrauli Road
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| 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 (24)
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| Relations |
| BioProject |
PRJNA316845 |
| SRA |
SRP072563 |
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