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Sample GSM3108730 Query DataSets for GSM3108730
Status Public on Apr 23, 2021
Title Input Mock
Sample type SRA
Source name Bladder cancer cells
Organism Homo sapiens
Characteristics cell line: 5637 cells
chip antibody: none
agent: Mock
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
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.
BioSample SAMN08971280
SRA SRX3988555

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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