|
| Status |
Public on Jul 13, 2020 |
| Title |
HS5_R2 |
| Sample type |
SRA |
| |
|
| Source name |
Seed
|
| Organism |
Cicer arietinum |
| Characteristics |
genotype: Himchana 1
tissue: Seed
development stage: Mid_maturation_(S5)
|
| Growth protocol |
Plants were grown in natural field conditions and seeds undergoing late-embryogenesis (S3) and mid-maturation (S5) stages of seed development were harvested from field-grown plants.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from seeds using Qiagen's DNeasy Plant mini-kit.
Genomic DNA samples were fragmented via sonication, end repired and adapters were ligated. The adapter-ligated DNA fragments were used for bisulphite conversion using EZ DNA Methylation-Gold kit. After size selection libraries were prepared using Illumina protocol.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw data was filtered to remove adapter sequences and low-quality reads using NGS QC Toolkit (v2.3).
High-quality filtered reads were aligned to kabuli chickpea genome (v1) using Bismark (v0.14.3) and clonal reads were removed.
Uniquely mapped reads were used to determine methylated cytosines (mCs) using methylKit (v0.9.2).
mCs were identified showing ≤ 0.001 significance and covered with ≥ 5 reads at a cytosine site in the chickpea genome.
Genome_build: kabuli chickpea genome (v1)
Supplementary_files_format_and_content: tab delimited text files including methylated cytosine position
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Mukesh Jain |
| Phone |
91-11-26704686
|
| Organization name |
Jawaharlal Nehru University
|
| Street address |
New Mehrauli Road
|
| City |
New Delhi |
| State/province |
New Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL20619 |
| Series (1) |
| GSE131669 |
DNA methylation during seed development in small-seeded chickpea |
|
| Relations |
| BioSample |
SAMN11834622 |
| SRA |
SRX5884705 |
