|
| Status |
Public on Apr 10, 2024 |
| Title |
WT_rep3, BS-seq |
| Sample type |
SRA |
| |
|
| Source name |
14-day-old seedlings
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 14-day-old seedlings
cultivar: Nipponbare
genotype: wild-type
treatment: no treatment
|
| Growth protocol |
Rice were grown in artificial growth chambers under an SD photoperiod for 14 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
14-day-old rice seedlings were harvested and total genomic DNA was extracted using the DNeasy plant maxi kit (QIAGEN).
Sodium bisulfite treatment, library construction, and sequencing were performed via the custom service of GENERGY BIO (Shanghai, China).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Oryza sativa Nipponbare
WT_BS_rep3
BS-Seq/Bisulfite-seq/whole-genome bisulfite sequencing (WGBS)
|
| Data processing |
Cutadapt was used to trim paired-end reads to obtain high-quality reads (q ≥ 20) with no adapter.
Bismark was used to map filtered reads to the rice reference genome (MSU7) and to obtain DNA methylation regions (DMRs) from filtered mapping results.
The DNA methylation levels were extracted and visualized by using ViewBS.
Assembly: MSU7
Supplementary files format and content: Bismark coverage files containing DNA methylation calls.
|
| |
|
| Submission date |
Apr 05, 2024 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Wenhao Xie |
| E-mail(s) |
[email protected]
|
| Phone |
18005879367
|
| Organization name |
Fudan University
|
| Department |
School of Life Science
|
| Street address |
No. 2005, Songhu Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (2) |
| GSE225483 |
BSseq for WT and osino80 |
| GSE263341 |
ChIP-seq, RNA-seq and BS-seq for WT and osino80 |
|
| Relations |
| BioSample |
SAMN40763875 |
| SRA |
SRX24172870 |
