|
| Status |
Public on Mar 30, 2015 |
| Title |
HEK293 cells IgG control ChIP (2514-WPT-24_1) |
| Sample type |
SRA |
| |
|
| Source name |
cultured cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293 cells
chip antibody: Purified rabbit IgG (Bethyl P120-101)
|
| Growth protocol |
HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum, 100 Iu/ml penicillin, and 100 ug/ml streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After crosslinking and quenching of formaldehyde, lysates were prepared, sonicated to give a mean chromatin length of 200 bp, cleared by centrifugation, and cleared lysates subjected to reaction with antibodies (or IgG control) overnight.
ChIP DNA was converted into an Illumina sequencing library using the NEBNext Ultra DNA Library Prep Kit (for Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following configurations: m(1), -3(1).
Peaks were called using SPP peak caller version 1.10.1 with the following setting: Npeak(300000), x(-500:85).
An IDR threshold of 0.5% was applied to pooled pseudoreplicates to get final sets of peaks.
Peaks that overlap with the blacklisted genomic regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include peaks called in samples.
|
| |
|
| Submission date |
Aug 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Qingguo Wang |
| E-mail(s) |
josephw10000@gmail.com
|
| Organization name |
Vanderbilt University
|
| Department |
Biomedical Informatics
|
| Street address |
2525 West End AVE Suite 808
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37221 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE60897 |
Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC |
|
| Relations |
| BioSample |
SAMN03012850 |
| SRA |
SRX689367 |
