|
| Status |
Public on Jun 11, 2019 |
| Title |
ChIP-seq_CDK8_IFNg |
| Sample type |
SRA |
| |
|
| Source name |
Primary human monocyte-derived macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: monocytes
treatment: IFNg
|
| Treatment protocol |
Cells were treated with or without IFN-γ (100 U/ml) for 48 hours and then stimulated with LPS (10 ng/ml) for 3 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 |
| |
|
| Description |
antibody: anti-CDK8 (Santa Cruz sc-1521)
|
| 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 4.9.1, Heinz et al., 2010) was used to generate bigWig files.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Oct 08, 2018 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Keunsoo Kang |
| E-mail(s) |
kangk1204@gmail.com
|
| Organization name |
Dankook University
|
| Street address |
119 Dandae-ro
|
| City |
Cheonan |
| ZIP/Postal code |
31119 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE120943 |
IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [ChIP-seq] |
| GSE120945 |
IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization |
|
| Relations |
| BioSample |
SAMN10218708 |
| SRA |
SRX4813037 |
