|
| Status |
Public on May 23, 2024 |
| Title |
Col-0_G10_rep5 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: wildtype
generation: G10
|
| Growth protocol |
Plants were grown on soil under long day conditions (23 °C, 16h light, 8h dark)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Three-week-old seedlings were collected for genomic DNA extraction using DNeasy Plant Maxi Kit (Qiagen, 68163)
Genomic DNA was processed at the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China). Libraries were prepared for bisulfite sequencing according to the manufacturer’s (Illumina) instructions and were sequenced on an Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For data analysis, low base quality reads were trimmed using Trimmomatic with parameter "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". The remaining high quality sequences were mapped to Arabidopsis reference genome using BSMAP.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bigWig files give methylation level for Cs with depth >= 4. 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 |
Feb 08, 2021 |
| Last update date |
May 23, 2024 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
|
| Street address |
625 Agriculture Mall Dr.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE166343 |
Active DNA demethylation controls transgenerational epigenetic stability |
|
| Relations |
| BioSample |
SAMN17833613 |
| SRA |
SRX10047109 |
