|
| Status |
Public on Jun 14, 2020 |
| Title |
siz1-2_BS |
| Sample type |
SRA |
| |
|
| Source name |
14-day-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: siz1-2 mutant
tissue: seedlings
|
| Growth protocol |
Seedlings were grown on 1/2 MS medium with 1% sucrose and 0.5% agar
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 14-day-old seedlings using the DNeasy Plant Maxi Kit (Qiagen, 68163) and sent to the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) for bisulfite treatment. Libraries were prepared for sequencing according to the manufacturer’s (Illumina) instructions and sequenced on an Illumina Hiseq 2500 platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
treated with bisulfite
|
| Data processing |
MethylC-Seq： For data analysis, data were trimmed using trimmomatic with parameter "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". Clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP with parameter "-m 0 -x 1000 -w 2", and python script of BSMAP was used to remove potential PCR duplicates and extract methylation ratios.
Genome_build: TAIR10
Supplementary_files_format_and_content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) 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 |
Jun 13, 2020 |
| Last update date |
Jun 15, 2020 |
| 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) |
| GSE152425 |
SIZ1-mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN15230438 |
| SRA |
SRX8541172 |
