|
| Status |
Public on Apr 23, 2021 |
| Title |
Input Decitabine and Cisplatin |
| Sample type |
SRA |
| |
|
| Source name |
Bladder cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 5637 cells
chip antibody: none
agent: Decitabine and Cisplatin
|
| Treatment protocol |
5637 cells were treated with 100nM DEC or with DEC and cisplatin combined daily for 72 hours
|
| Growth protocol |
10% FBS in DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10–50 mg of genomic DNA for each sample was sonicated and used for the ligation of barcoded Illumina adapters. A total of 5 mg adaptor ligated DNA was used for immunoprecipitation by 5-Methylcytosine (5-mC) Rabbit mAb (Cell Signaling 28692S).
Sequencing libraries were generated using a DNA SMART ChIP-Seq Kit (Clonetech 634865) and pooling immunoprecipitated DNA from 3 independent samples.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: wig file
|
| |
|
| Submission date |
Apr 23, 2018 |
| Last update date |
Apr 23, 2021 |
| Contact name |
Jiong Li |
| E-mail(s) |
[email protected]
|
| Phone |
3105617186
|
| Organization name |
UCLA
|
| Department |
School of Dentistry
|
| Lab |
Cunyu Wang
|
| Street address |
33-030 CHS
|
| City |
Los Angeles |
| State/province |
CA - California |
| ZIP/Postal code |
91406 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE113537 |
Genome-wide DNA methylation maps of Decitabine and/or Cisplatin treated bladder cancer cells. |
|
| Relations |
| BioSample |
SAMN08971276 |
| SRA |
SRX3988559 |
