|
| Status |
Public on Apr 08, 2015 |
| Title |
H3K27ac_Macrophage-control_250 |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage-control
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control buffer
gender: male
cell type: Macrophage
chip antibody: rabbit polyclonal anti-H3K27ac (ab4729, Abcam)
|
| Treatment protocol |
After 7 days of culture cells were treated for 48 hours with either oxLDL (50mcg/ml, Copper oxidized, endotoxin-free) or control buffer which lacked oxLDL
|
| Growth protocol |
CD14 positive monocytes were isolated by positive selection from peripheral blood from healthy volunteers. Monocytes were cultured for 7 days with 50ng/ml macrophage colony stimulating factor to generate macrophages.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H3K27ac enriched genomic DNA and input control DNA (no antibody) was extracted using the Invitrogen Magnify Kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA) with rabbit polyclonal anti-H3K27ac (ab4729, Abcam, Cambridge, MA).
Libraries were generated from gel-purified ~200bp DNA fragments. After adapter ligation and PCR-based amplification, samples were multiplexed into one lane of the Illumina HiSeq platform to generate paired end 50bp reads (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: macs_H3K27ac_macrophage_peaks.bed
processed data file: diffreps_H3K27ac.txt
|
| Data processing |
Base calls were generated using a Illumina basecaller bcl2fastq, version 1.8.4
Reads were mapped to the UCSC hg19 reference genome (with a canonical haplotype) using STAMPY v1.021 with default parameters.
Mapped reads were filtered in SAMTOOLS based on a minimum MAPQ score of 15.
For subsequent data analysis paired end files were converted to single end by retaining one read of each proper pair and all improperly paired reads and reads from ENCODE blacklisted sites were removed.
Peak calling was performed using MACS1.4.2 (with background input control DNA) on pooled replicates and dynamic enhancer sites were identified with Diffreps V1.55 (window 500bp, step 50bp, two biological replicates, negative binomial based statistical test, FDR 2.5%).
Genome_build: UCSC hg19 (Canonical haplotype)
Supplementary_files_format_and_content: MACS files are in BED format and comprise peaks that identify enhancers sites (and promoters). Diffreps output is in tab delimited text file output and comprises dynamic enhancer sites (and promoters).
|
| |
|
| Submission date |
Feb 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher O'Callaghan |
| E-mail(s) |
chris.ocallaghan@ndm.ox.ac.uk
|
| Phone |
+44 (0)1865 287794
|
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Medicine
|
| Lab |
O'Callaghan Lab - Henry Wellcome Building for Molecular Physiology
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE54972 |
Chromatin immunoprecipitation with next generation sequencing (ChIP-seq) of H3K27ac in primary human macrophages and foam cells |
| GSE54975 |
Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease associated variant that regulates PPAP2B expression through altered C/EBP-beta binding |
|
| Relations |
| BioSample |
SAMN02641264 |
| SRA |
SRX470221 |
