|
| Status |
Public on Apr 10, 2021 |
| Title |
Col-0_BS-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col-0 wild type
tissue: Seedlings
|
| Growth protocol |
Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose.
|
| 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, 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 4000 |
| |
|
| Description |
treated with bisulfite
|
| Data processing |
Adapters were trimmed by cutadapt (version 1.16) and low-quality sequences (q < 20) using trimmomatic (version 0.36).
Clean reads were then mapped to the Arabidopsis thaliana TAIR 10 genome using BSMAP (2.90) with default parameters
methratio.py script was used to extract the methylation ratio from BSMAP mapping results, the option -r was used to remove potential PCR duplicates.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bigWig files give methylation level for all Cs(three contexts). Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).
|
| |
|
| Submission date |
Apr 09, 2021 |
| Last update date |
Apr 11, 2021 |
| Contact name |
Pei Huang |
| Organization name |
Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai
|
| Street address |
Fenglin Road 300
|
| City |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE171805 |
FVE regulates DNA methylation levels at a subset of RdDM loci. |
|
| Relations |
| BioSample |
SAMN18686483 |
| SRA |
SRX10566676 |
