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| Status |
Public on Jun 25, 2021 |
| Title |
PPs3 (Bisulfite-Seq) |
| Sample type |
SRA |
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| Source name |
Colonic epithelia
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: colon
gender: male
treatment: PPs-treated rats
cell type: Colonic epithelia
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Colonic epithelia (>95%) were obtained by scraping at 4 0C . Genome DNA was extracted with gDNA Extraction Kit (Omega Bio-Tek Research，USA) and sheared to fragments of 150-200 bp (Covaris E-series instrument, Australia).
DNA libraries were prepared with Agilent SureSelectXT Methyl-seq Library Pre kit and then hybridized with hybridization reagents, blocking agents and the SureSelect capture library.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw data were trimmed by Trim galore v0.4.1 to produce clean data (clean reads).
The clean reads were processed by Bismark v0.15.0 for genome alignment (Rat6) and the PCR duplicates were removed.The information of cytosine (C), CpG C and methylated CpG C (5mC), as well as their distribution and frequency, can be extracted from the information of genome alignment.
The methylation level of 5mC is calculated by C/C+T(frequency).
The reads with more than 10X read depth were then processed by R methylkit v0.9.5 to indicate the details of the read depth and methylation level of all 5mC.
The methylation level of 5mC between groups were compared and annotated by DSS Bioconductor package, and the 5mC with mean methylation level difference > 10% and p < 0.05 between groups was considered to be differentially methylated site (DMS).
Genome_build: Rat6
Supplementary_files_format_and_content: text files report methylation freq
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| Submission date |
Oct 13, 2020 |
| Last update date |
Jun 29, 2021 |
| Contact name |
Ruiqiang Yan |
| E-mail(s) |
ruiqiang_yan@shbio.com
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| Organization name |
Jinan University
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| Street address |
黄埔大道西601号
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| City |
guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE159439 |
MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats [Bisulfite-Seq] |
| GSE159440 |
MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats |
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| Relations |
| BioSample |
SAMN16428005 |
| SRA |
SRX9285475 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4829874_PPs3_CHG.txt.gz |
63.2 Mb |
(ftp)(http) |
TXT |
| GSM4829874_PPs3_CHH.txt.gz |
175.1 Mb |
(ftp)(http) |
TXT |
| GSM4829874_PPs3_CpG.txt.gz |
26.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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