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Status |
Public on Jul 07, 2017 |
Title |
RXR ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep1) |
Sample type |
SRA |
|
|
Source name |
RXR ChIP-seq, differentiating macrophages treated with IL-4
|
Organism |
Homo sapiens |
Characteristics |
age: adult tissue: blood cell type: PBMC-derived differentiating macrophages treatment: IL-4 chip antibody: RXR (sc-774) lot#E0213
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Human CD14+ monocyte-derived differentiating macrophages at 24 hours following isolation were treated with IL-4 (20 ng/ml, 30 min) as indicated then harvested by scraping in medium followed by centrifugation at 4C for 10 min at 1000 g then cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP. Chromatin was immunoprecipitated with antibodies against PU.1 (sc-352), STAT6 (sc-981), RXR (sc-774) and H3K27Ac (ab4729). Library preparation was performed as previously described (Nagy, Daniel, Jonas et al., 2013) with minor modifications. 1 ng (STAT6, PU.1, RXR) and 5 ng (H3K27Ac) DNA amounts were used for the library preparation.
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
hs_MQ_IL4_RXR_rep1
|
Data processing |
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
peak/region calling with homer v4.2 findPeaks using -center or -region -size 1000 -minDist 2500 parameters, respectively
annotation with homer v4.2 annotatePeaks.pl using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: [ChIP-seq] annotation file
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|
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Submission date |
Jul 06, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Gergely Nagy |
Organization name |
University of Debrecen
|
Department |
Department of Biochemistry and Molecular Biology
|
Street address |
Egyetem ter 1.
|
City |
Debrecen |
ZIP/Postal code |
4032 |
Country |
Hungary |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE100889 |
Extensive overlap of the STAT6 and RXR cistromes in the active enhancer repertoire of human CD14+ monocyte-derived differentiating macrophages |
|
Relations |
BioSample |
SAMN06578761 |
SRA |
SRX2638280 |