|
| Status |
Public on Jun 11, 2018 |
| Title |
AOMDSSCurcumin_1 [Bisulfite-seq] |
| Sample type |
SRA |
| |
|
| Source name |
colon epithelial cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Colon
age: 18 weeks
group: AOM and DSS induced plus curcumin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All the colons were flushed with ice-cold saline to remove feces and opened longitudinally on filter paper. The proximal segment and tumors of the right portion of the colon were removed, then colon epithelial cells were isolated from the remaining tissues using a scraping method as previously described. Briefly, the tissues were scraped using a glass slide on ice and the mucosal scrapings were resuspended in ice cold PBS. The remaining tissue after scraping was snap frozen and stored for further analyses. The epithelial preparations were centrifuged at low-speed (150x g) and washed with ice cold PBS twice to reduce blood cell contamination. Isolated epithelial cells were pelleted, snap frozen with dry ice, then store at -80°C for further analysis.
DNA libraries were prepared for sequencing using Agilent SureSelectXT Mouse Methyl-Seq system. (Catlog number 931052)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina standard procedure for basecalling.
The reads were aligned to the in silico bisulfite-converted mouse genome (mm9) with the Bismark (version 0.15.0) alignment algorithm.
After alignment, DMRfinder (version 0.1) was used to extract methylation counts and cluster CpG sites into differentially methylated regions (DMRs)
Each DMR contains at least five CpG sites. Methylation differences greater than 0.10 and with a p-value smaller than 0.05 were considered significant.
Genomic annotation was performed by ChIPseeker (version 1.10.3) in R (version 3.4.0)
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited tables of counts of methylation and unmethylation for each DMR (differentially methylated region).
|
| |
|
| Submission date |
Aug 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Renyi Wu |
| E-mail(s) |
renyiwu@gmail.com
|
| Organization name |
Rutgers University
|
| Department |
Pharmacy School
|
| Lab |
013
|
| Street address |
160 Frelinghuysen road
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE102645 |
Methylome Changes During the Progression of Colitis-accelerated Colon Cancer in Mouse and the Blockage by Curcumin |
| GSE102648 |
Transcriptome and Methylome Changes During the Progression of Colitis-accelerated Colon Cancer in Mouse and the Blockage by Curcumin |
|
| Relations |
| BioSample |
SAMN07504490 |
| SRA |
SRX3092848 |
