|
| Status |
Public on Jul 15, 2018 |
| Title |
Wild leaf |
| Sample type |
SRA |
| |
|
| Source name |
Wild leaf
|
| Organism |
Cicer reticulatum |
| Characteristics |
genotype: PI 489777 (wild)
tissue: Wild leaf
|
| Growth protocol |
For root tissues, plants were grown in a culture-room maintained at a maximum temperature of 22 ± 1 °C and a minimum of 12 ± 1 °C, and relative humidity of 60% under continuous light (200 μE m−2 s−1) for 15 days. Other tissues (leaves, flowers and young pods of cultivated chickpea and leaves of wild chickpea) were harvested from the field-grown mature plants.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using Qiagen DNeasy Minikit. DNA samples were fragmented via sonication to generate 100-300bp fragments. The fragments were end repaired, followed by ligation with TruSeq-methylated adapters. 500ng adapter-ligated DNA fragments were used for bisulphite conversion using EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) according to the manufacturer's instructions. Library quality was analyzed after desalting, size selection and PCR amplification.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The sequence data was filtered for adapter sequences and low-quality reads using NGS QC Toolkit (v2.3).
The quality filtered reads from each sample were aligned to the kabuli chickpea genome (v1.0) using Bismark (v0.14.3). Only the uniquely aligned reads were retained.
The mapped reads on the genome were used as input in methylKit (v0.9.2).
Identification of mCs was performed with minimum read coverage of ≥ 5 and P-value ≤ 0.0001.
Genome_build: Chickea genome (v1.0)
Supplementary_files_format_and_content: Methylated cytosines
|
| |
|
| Submission date |
Sep 06, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL23991 |
| Series (1) |
| GSE103575 |
Single-base resolution DNA methylome maps of different organs in chickpea |
|
| Relations |
| BioSample |
SAMN07611877 |
| SRA |
SRX3165523 |
