|
| Status |
Public on Dec 06, 2020 |
| Title |
WT_Rep1_BS-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 14-d-old seedlings and sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
treated with bisulfite
|
| Data processing |
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to TAIR10 using BSMAP 2.87 with parameters -g 1
methratio.py python script of BSMAP was used to extract metylation ratios from BSMAP results with parameters -z and -r
Genome_build: TAIR10
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Dec 06, 2017 |
| Last update date |
Dec 06, 2020 |
| Contact name |
Huang Huan |
| E-mail(s) |
ahuanghuan@163.com
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Center for Plant Stress Biology
|
| Street address |
No. 3888 Chenhua Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE107751 |
The SWR1 Complex Regulates Active DNA Demethylation in Arabidopsis |
| GSE107752 |
35S-SUC2 WT and antisilencing mutants |
|
| Relations |
| BioSample |
SAMN08136773 |
| SRA |
SRX3447393 |
