|
| Status |
Public on May 02, 2015 |
| Title |
MCF7 Veh rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human breast adenocarcinoma cell line
passages: 20-30
chip-seq antibody: Anti-acetyl-histone H4 (Lys12) (07-595; EMD Millipore) (1 µg used)
cell line: MCF7
|
| Treatment protocol |
After 2 days of hormone deprivation, vehicle (ethanol - Veh) was added as negative control.
|
| 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) and 1% penicillin/streptomycin. After one day of cell-splitting, the media was changed to DMEM containing 5% charcoal-dextran treated FBS (Biochrome).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M 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 NextSeq 500 |
| |
|
| Description |
Cells were crosslinked with 1 % formaldehyde for 10 minutes.
MCF7_H4K12ac_Veh.bigwig
|
| Data processing |
The reads were mapped to the human reference genome (UCSC HG19) using Bowtie (version 1.0.0) (Langmead et al., 2009).
DeepTools (Ramírez et. al., 2014) was used to create bigwigs by normalizing the ChIP-seq sample with the input samples of each cell line and obtaining the ratio of the reads using bamCompare function. sample.
Normalization was done using read counts of each ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were made from bamCompare function of deepTools. Scores represent ratio of the number of reads relative to input.
|
| |
|
| Submission date |
Feb 12, 2015 |
| 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 |
GPL18573 |
| Series (1) |
| GSE65886 |
H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription |
|
| Relations |
| BioSample |
SAMN03342090 |
| SRA |
SRX876018 |
