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Sample GSM2845729 Query DataSets for GSM2845729
Status Public on Nov 10, 2017
Title C/EBPa ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics treatment: cells differentiated in the presence of MCSF
age: 8-12 weeks
tissue: bone marrow-derived macrophages
chip antibody: CEBPa (sc-61X)
Treatment protocol Cells were polarized on the 6th day of the differentiation with IL-4 (20ng/ml) for the indicated period of time.
Growth protocol Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.
Extracted molecule genomic DNA
Extraction protocol Mouse bone marrow-derived macrophages were cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP.
Libraries were prepared either with Ovation Ultralow Library Systems (Nugen) or TruSeq ChIP library systems (Illumina) according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description mm_BMDM_veh_CEBPa
Data processing Samples were aligned by bwa v0.7.10 using default parameters.
Bam files were generated and indexed with samtools v0.1.19 using default parameters.
Tag directories were generated with homer v4.2 makeTagDirectory using -checkGC parameter.
Region calling for histone ChIP-seq samples was done with homer v4.2 findPeaks using -center -size 1000 -minDist 2500 parameters.
Peak calling for ATAC-seq and factor ChIP-seq samples was done with macs2 2.0.10 using -B --SPMR parameters.
mm10 ENCODE blacklist were subtracted from the peak lists.
Annotation was created with homer v4.2 annotatePeaks.pl using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: annotation file
 
Submission date Nov 08, 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 GPL17021
Series (2)
GSE106705 Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [ChIP-Seq II]
GSE106706 Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization
Relations
BioSample SAMN04868774
SRA SRX2196773

Supplementary file Size Download File type/resource
GSM2845729_annotated_mm_BMDM_veh_CEBPa_macs_peaks_vs_bl.tsv.gz 1.9 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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