|
| Status |
Public on Dec 25, 2017 |
| Title |
Control BRD4_ChIP-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Control BRD4_ChIP-seq
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
cell type: Vascular Smooth Muscle Cells (VSMCs)
passages: 3-6
treated with: none
chip antibody: BRD4 (Cat. No. A301-985A100; Bethyl, Montgomery, TX
|
| Treatment protocol |
Angiotensin (Ang II) treatment, RVSMCs were serum depleted in M199 medium containing 0.2% BSA for 48h and stimulated without (control) or with 100 nM Ang II (Bachem) for indicated time periods.
|
| Growth protocol |
Rat Vascular smooth muscle cells were cultured in M199 (PAA) medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies.
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. Briefly, 10 ng of immunoprecipitated DNA was end-repaired (Epicenture), and a single adenosine was added using Klenow exo- (New England Biolabs (NEB)) and ligated to Illumina adaptor oligonucleotides (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
Paired-end ChIP-seq reads were aligned to the rn4 genome assembly using bowtie2 ( version 2.1.0) with the following parameters --phred33 --local -N 1
peaks were called using MACS2 version 2.1.1.20160309 with the following parameters --broad -g mm -p 0.05 -f BAM -B
Genome_build: rn4
Supplementary_files_format_and_content: tdf (tiled data file) coverage file generated by igvtools which is the binary read count density file for faster display in IGV.
|
| |
|
| Submission date |
Feb 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nancy Chen |
| E-mail(s) |
zhuchen@coh.org
|
| Organization name |
City of Hope
|
| Department |
Diabetes
|
| Street address |
1500 Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE95067 |
Regulation of Angiotensin II Actions by Enhancers and Super-enhancers in Vascular Smooth Muscle Cells |
|
| Relations |
| BioSample |
SAMN06347989 |
| SRA |
SRX2576589 |
