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Sample GSM2695657 Query DataSets for GSM2695657
Status Public on Jul 07, 2017
Title RXR ChIP-seq analysis of human differentiating macrophages treated with IL-4 (rep2)
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description hs_MQ_IL4_RXR_rep2
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
 
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 SRX2638279

Supplementary file Size Download File type/resource
GSM2695657_hs_MQ_IL4_RXR_rep2_annot.txt.gz 632.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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