|
| Status |
Public on Apr 08, 2015 |
| Title |
FAIRE_seq_Macrophage-oxLDL_277 |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage-oxLDL
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: oxLDL(50mcg/ml)
gender: male
cell type: Macrophage
|
| 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 50ml of 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 |
FAIRE enriched genomic DNA was extracted using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).
Libraries were generated from gel-purified ~200bp DNA fragments (actual fragment size median 151bp +-39 median absolute deviation (MAD) for samples numbered 279, 280, 277, 278 and 141+-32 MAD for samples 205, 207). After adapter ligation and PCR-based amplification, samples were sequenced on the Illumina HiSeq platform to generated paired end 50bp reads (Illumina, San Diego, CA). Samples were multiplexed across 2 lanes.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: fseq_foam_cells.bed
processed data file: FAIRE_diffreps_FDR2.5.txt
processed data file: dynamic_FAIRE_hotspots.bed
|
| Data processing |
Base calls were generated using a standard Illumina HiSeq pipeline using Bustard 1.9.3
Reads were mapped to the UCSC genome browser 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 FSEQ on pooled replicates (V1.84, default parameters, peaks merged if within 140bp (fragment size) and removed if < 50bp or >5kb in width. The top 100k peaks were retained) and dynamic FAIRE-seq sites were identified on pooled biological replicates using Diffreps V1.55 (200bp windows, 20bp step, G-test, FDR < 2.5%)
Genome_build: UCSC hg19 (Canonical haplotype)
Supplementary_files_format_and_content: FSEQ files are in BED format and comprise peaks that identify open chromatin sites [column headers are: Chromosome, start, end, peak_signal, peak_width]. Diffreps output is in tab delimited text file output and comprises 13,516 dynamic chromatin sites. Dynamic FAIRE hotspots are in BED format and comprise hotspots of dynamic chromatin identified by Diffreps with p value < 0.05
|
| |
|
| 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) |
| GSE54971 |
Formaldehyde-assisted isolation of regulatory elements with next generation sequencing (FAIRE-seq) 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 |
SAMN02641260 |
| SRA |
SRX470218 |
