|
| Status |
Public on Jul 10, 2014 |
| Title |
H2Bub1 Veh rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human breast adenocarcinoma
cell line: MCF7
passages: 20-30
chip-seq antibody: H2Bub1 D11 (5546 from Cell signaling, 1.5 µL used)
|
| Treatment protocol |
After 2 days of hormone deprivation, MCF7 cells were treated with 30 minutes of 150 nM JQ1 treatment prior to 10 nmol/L 17-β-estradiol (Sigma-Aldrich) treatment for 2 hours. DMSO and vehicle were added as negative controls.
|
| Growth protocol |
MCF7 cells were grown in phenol red- free high-glucose Dulbecco's Modified Eagle's Media (DMEM; Invitrogen) with 10% bovine growth serum (Thermo Scientific). For estrogen induction experiments, after one day of cell-splitting, the media was changed to DMEM containing 5% charcoal-dextran treated FBS (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% Formaldehyde for 10 or 20 minutes and quenched with 125 mM Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cells were crosslinked with 1 % formaldehyde for 10 minutes.
|
| Data processing |
The reads were mapped to the human reference genome (UCSC HG19) using Bowtie (version 1.0.0) (Langmead et al., 2009).
Peak-calling was done by Model based analysis of ChIP-seq (MACS version 1.4.2) (Zhang et al., 2008).
Coverage was normalized on the total number of mapped reads per hundred million.
Genome_build: hg19
Supplementary_files_format_and_content: WIG, normalized
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven A Johnsen |
| E-mail(s) |
sjohnsen@alumni.mayo.edu
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Department of General, Visceral and Pediatric Surgery
|
| Street address |
Robert-Koch-Straße 40
|
| City |
Göttingen |
| State/province |
Niedersachsen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE55921 |
Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation [ChIP-seq] |
| GSE55923 |
Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation |
|
| Relations |
| BioSample |
SAMN02689280 |
| SRA |
SRX490440 |
