|
Status |
Public on Nov 10, 2017 |
Title |
p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep2) |
Sample type |
SRA |
|
|
Source name |
bone marrow
|
Organism |
Mus musculus |
Characteristics |
treatment: cells differentiated in the presence of MCSF (ctrl_1hLPS) age: 8-12 weeks tissue: bone marrow-derived macrophages chip antibody: p65 (sc-372)
|
Treatment protocol |
Mouse bone marrow-derived macrophages were treated with (1) IL-4 (20 ng/ml; 1, 6 or 24 hours) as indicated or (2) were pretreated with IL-4 (20 ng/ml) for 24 hours then LPS (100ng/ml) were added for 1 hours.
|
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_ctrl_1hLPS_p65_rep2
|
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) |
GSE106701 |
Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [ChIP-Seq I] |
GSE106706 |
Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization |
|
Relations |
BioSample |
SAMN04868774 |
SRA |
SRX3354486 |