|
| Status |
Public on Apr 08, 2015 |
| Title |
C/EBP beta_Macrophage-control_204 |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage-control
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control
cell type: Macrophage
chip antibody: C/EBP beta antibody (Santa Cruz, catalog# sc-150, lot# co513)
|
| Treatment protocol |
After 7 days cells were treated either with oxLDL 50mcg/ml or control buffer for 48 hours.
|
| Growth protocol |
CD14+ monocytes were isolated by positive selection from healthy, consenting adults and differentiated into macrophages over 7 days by culture with 50ng/ml macrophage colony stimulating factor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the Invitrogen Magnify ChIP kit according to the manufacturers instructions.
The libraries were prepped using the Apollo ChIP32 No Upper Cut, min lower cut protocol (non-GUI user maintenance protocol). We then did a further size selection (from an E-gel) which removed the >600bp contribution.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: macs2_macrophages_cells_peaks.txt
processed data file: diffreps_cebpb.txt
paired-end fastqs median absolute deviation: 57
|
| Data processing |
We used off-line base caller 1.8.4
Aligned to hs37d5 using Stampy
Filtered on MAPQ score 4 using Samtools to remove non-uniquely mapped reads
Duplicates removed using Picard 'removeduplicates' tool
One read of each proper pair and all 'improperly' paired reads taken to effectively convert to a single end file – using samtools
Bam files converted to bed files using BamToBed in the Bedtools suite.
Peaks called using MACS2 with default settings using pooled biological replicates for control or oxLDL treated cells. Dynamic sites were identified using diffreps version 1.55.4 with parameters – window size 200, step size 20, FDR 2.5%, Chi sqared test on pooled biological replicates, sites with less than a total of 50 normalized reads in macrophages and foam cells were excluded.
Genome_build: hs37d5
Supplementary_files_format_and_content: [MACS2_foam_cell_peaks.txt and MACS2_control_cell_peaks.txt] MACS2 output on pooled biological replicates for control cells or oxLDL treated cells.
Supplementary_files_format_and_content: [diffreps_cebpb.txt] Diffreps output
|
| |
|
| Submission date |
Feb 23, 2015 |
| 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 |
GPL16791 |
| Series (2) |
| 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 |
| GSE66192 |
A study of the effect of OxLDL on C/EBP beta binding in human macrophages using chromatin immunoprecipitation for C/EBP beta with high throughput sequencing (ChIP-seq) |
|
| Relations |
| BioSample |
SAMN03366091 |
| SRA |
SRX885894 |
