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| Status |
Public on Jul 13, 2020 |
| Title |
DNA methylation during seed development in small-seeded chickpea |
| Organism |
Cicer arietinum |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Genomic DNA was extracted from all the samples were fragmented to a mean size of 200-500 bp via sonication followed by sodium bisulphite conversion (DNA Methylation-GoldTM Kit, Zymo Research). TrueSeq-methylated adaptors were ligated and sequenced using Illumina HiSeq platform. Adapters and low-quality reads were removed using NGS QC Toolkit (v2.3). High-quality filtered reads were mapped on kabuli reference genome using Bismark (v0.14.3). Methylation level in each cytosine residue(s) and differentially methylated regions (DMRs) were detected using Methylkit (v0.5.6).
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| Contributor(s) |
Jain M, Garg R, Gupta K, Khemka N, Rajkumar MS |
| Citation(s) |
32620865 |
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| Submission date |
May 22, 2019 |
| 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 (5)
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| Relations |
| BioProject |
PRJNA544333 |
| SRA |
SRP199248 |
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