|
| Status |
Public on Feb 15, 2023 |
| Title |
ST-S2 WGBS |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Cicer arietinum |
| Characteristics |
condition: Stress
genotype: JG62
age: 18 days old
|
| Treatment protocol |
Salinity stress was given to 12 days old seedlings with 80mM NaCl for 6 days on alternate days. The roots were harvested from 18 day old plants from both stressed and control samples.
|
| Growth protocol |
Cicer arietinum ICCV2 and JG62 seedlings were grown in growth chamber
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from all the samples using Qiagen DNeasy kit. The extracted DNA were quantified using Qubit 2.0 Fluorometer and quality was accessed in Bioanalyzer.
DNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ST-S2
BS-seq
|
| Data processing |
The FASTQ files obtained from BS-sequencing were pre-processed using NGS QC Toolkit (v2.3) to remove adapters and low-quality reads below 20 Phred score.
Filtered high-quality reads were mapped on the Kabuli chickpea genome (v1.0) using Bismark (v0.14.3).
Identification of methylated cytosines in different sequence context was determined using Methylkit (v1.5.3) with minimum read coverage of ≥ 3 and P-value ≤ 0.0001.
Assembly: Kabuli chickpea genome (v1.0) (https://data.legumeinfo.org/Cicer/arietinum/genomes/CDCFrontier.gnm1.GkHc/) (BIOPROJECT:PRJNA175619)
|
| |
|
| Submission date |
May 24, 2022 |
| Last update date |
Feb 15, 2023 |
| Contact name |
Rohini Garg |
| E-mail(s) |
[email protected]
|
| Phone |
09560056446
|
| Organization name |
Shiv Nadar University
|
| Street address |
Shiv Nadar University, NH - 91, Tehsil Dadri
|
| City |
Gautam Buddha Nagar |
| State/province |
UP |
| ZIP/Postal code |
201314 |
| Country |
India |
| |
|
| Platform ID |
GPL32287 |
| Series (2) |
| GSE204729 |
Epigenetic regulation during salinity stress response in chickpea (WGBS) |
| GSE204730 |
Salinity stress response in chickpea |
|
| Relations |
| BioSample |
SAMN28639385 |
| SRA |
SRX15438210 |
