|
| Status |
Public on Oct 29, 2013 |
| Title |
col BS-seq |
| Sample type |
SRA |
| |
|
| Source name |
14-d-old entire seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: wild-type
tissue: 14-d-old entire seedlings
|
| Treatment protocol |
no special treatment
|
| Growth protocol |
Seeds are sown on MS media, and then treated at 4C overnight. Afterwards, plates are placed under light for germination and growth for 14 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with CTAB method from 14-d Arabidopsis seedlings. Then RNA is eliminated by RNaseI.
Five micrograms of genomic DNA was fragmented into 100-300bp by sonication approach. The fragments were blunt‐ended and phosphorylated, and a single ʹAʹ nucleotide was added to the 3ʹ ends of the fragments. Then the fragments were ligated to adaptors. The resulting DNAs were treated with ZYMO EZ DNA Methylation-Gold kit to finish bisulfite conversion. After DNAs were recovered from gel, PCR amplifications were performed to enrich those DNAs with proper sizes. Finally, the final purified products were quantitated prior to cluster generation.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
For data analysis, adapter and low quality sequences were trimmed and clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP but allowing up to 2 mismatches.
Identification of differentially methylated regions (DMRs) was conducted according to reference (1) (Ausin et al., 2012) with modifications. In brief, only cytosines with a depth of at least 4 in libraries were retained for further analysis.
DNA methylation levels in every 200-bp windows with a step size of 50 bp were compared between wild-type and mutant plants using Fisher’s exact test with a p-value cutoff of 0.05. The p-values were then adjusted using the Benjamini-Hochberg method to control for FDRs.
Windows with ≥7DMCs (differentially methylated cytosines, defined as C with p<0.01 in Fisher’s exact test) and ≥1.5 fold change in DNA methylation levels were retained and combined if gap size is not more than 200 bp to generate DMRs.
Finally, the lengths of DMRs were adjusted to be from the first mC to the last mC.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files report methylation ratios
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lan Yang |
| E-mail(s) |
yanglbio@gmail.com
|
| Organization name |
Institute of Plant Physiol & Ecology, Chinese Academy of Sciences
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE51762 |
Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [BS-Seq] |
| GSE51764 |
Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Pattern |
|
| Relations |
| BioSample |
SAMN02384875 |
| SRA |
SRX368793 |
