|
Status |
Public on Jul 01, 2017 |
Title |
C/EBPB_Resting_rep2 |
Sample type |
SRA |
|
|
Source name |
Primary human monocyte-derived macrophages, untreated, C/EBPB ChIP
|
Organism |
Homo sapiens |
Characteristics |
disease state: healthy tissue: peripheral blood cell type: primary human monocyte-derived macrophages treatment: none chip antibody: anti-C/EBPB (Santa Cruz sc-150)
|
Treatment protocol |
Cells were treated with or without IFN-γ (100U/ml) for 48 hours.
|
Growth protocol |
Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore). Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 (version 2.2.5, Langmead et al., 2012 Nat Methods) with default parameters. HOMER (version 4.7.2, Heinz et al., 2010) was used to identify peaks of ChIP-seq enrichment over background. A false discovery rate (FDR) threshold of 0.001 was used for all data sets. Genome_build: hg19 (GRCh37) Supplementary_files_format_and_content: Bed files.
|
|
|
Submission date |
Apr 30, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Lionel B. Ivashkiv |
Organization name |
Hospital for Special Surgery
|
Street address |
535 East 70th Street
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10021 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE98367 |
IFN-γ Represses M2 Gene Expression in Human Macrophages by Suppressing and Disassembling MAF-binding Enhancers [ChIP-seq] |
GSE98369 |
Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF |
|
Relations |
BioSample |
SAMN06853939 |
SRA |
SRX2770847 |