|
| Status |
Public on Nov 01, 2017 |
| Title |
22Rv1_Veh_HNF4G IP |
| Sample type |
SRA |
| |
|
| Source name |
22rV1HNF4Gs_HNF4G IP
|
| Organism |
Homo sapiens |
| Characteristics |
hnf4g status: wildtype
ip: HNF4G
cell line: 22Rv1
|
| Treatment protocol |
Cells were harvested in log phase growth
|
| Growth protocol |
Cells were grown in 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was isolated and sheared. Following antibodies were used; HNF4G (Sigma; HPA005438 or Proteintech; 25801-1-AP); H3K4me1 (Abcam; ab8895); H3K27ac (Abcam; ab4729); AR (Abcam, ab108341); FOXA1 (Abcam; ab5089). Magnetic protein A/G beadswere used to collect immunoprecipitates. The immunoprecipate was washed and eluted using standing conditions.
Purified ChIP DNA was blunt-ended, ligated to adaptors, amplified with 8-12-cycles of PCR, and sequenced.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The sequenced reads from fastq files were mapped to hg19 using Bowtie 1.0
Peaks were called using MACS2. Downstream analysis were performed using Homer and SeqMiner
Genome_build: Hg19
Supplementary_files_format_and_content: ENCODE narrowPeak: Narrow (or Point-Source) Peaks format. See https://genome.ucsc.edu/FAQ/FAQformat.html
|
| |
|
| Submission date |
Aug 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shipra Shukla |
| E-mail(s) |
shuklas@mskcc.org
|
| Organization name |
MSKCC
|
| Street address |
417 East 68th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE85558 |
HNF4G, AR, FOXA1, H3K4me1, H3K27acetyl binding sites upon knockdown and overexpression of HNF4G in 22Rv1 and LNCaP prostate cancer cells respectively |
| GSE85559 |
Expression profiling and occupancy after knockdown or over-expression of HFN1A or HNF4G in prostate cancer cells |
|
| Relations |
| BioSample |
SAMN05570468 |
| SRA |
SRX2017944 |
