p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the pr... - SRA

SRX3354486: p65 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_1hLPS_rep2)
1 ILLUMINA (Illumina HiSeq 2500) run: 12.6M spots, 638.4M bases, 229.4Mb downloads

Design: Macrophages were double cross-linked with DSG (30min) and formaldehyde (10min). Nuclei were isolated using lysis buffer containing 0.15M NaCl, 0.005M EDTA pH 7.5, 0.05M Tris-HCl pH 7.5, 0.5% NP40, supplemented with protease inhibitor (Roche) prior to use. Chromtain was sheared with sonication and immunoprecipitated overnight using IgG (Millipore, 12-370) and antibodies against RXR (sc-774), P300 (sc-585), PU.1 (sc-352), RAD21 (ab992), STAT6 (sc-981) and PPARG (Persseuss #PP-A3409A). Chromatin-antibody complexes are extensively washed and eluted after pull-down by paramagnetic beads. Eluted complexes were decrosslinked overnight and purified by Minelute PCR Purification Kit. Immunoprecipitated DNA was quantified by Qubit fluorometer. Libraries were prepared from 5ng DNA either with Ovation Ultralow Library Systems (Nugen) or TruSeq ChIP library systems (Illumina) according to manufacturer_s instructions. Libraries were sequenced on HiSeq 2500.

Submitted by: University of Debrecen

Study: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage activation

PRJNA416285 • SRP123511 • All experiments • All runs

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The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4 activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. Repression results in decreased lineage-determining transcription factor, p300 coactivator and RNA polymerase II binding followed by reduced enhancer RNA expression, H3K27 acetylation and chromatin accessibility. In addition, STAT6-repressed enhancers showed extensive overlap with the NF-?B p65 transcription factor cistrome and exhibited decreased responsiveness to lipopolysaccharide after IL-4 stimulus on a subset of genes.

Sample:

SAMN04868774 • SRS1405681 • All experiments • All runs

Organism: Mus musculus

Library:

Name: mm_BMDM_ctrl_1hLPS_p65_rep2

Instrument: Illumina HiSeq 2500

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Runs: 1 run, 12.6M spots, 638.4M bases, 229.4Mb

Run	# of Spots	# of Bases	Size	Published
SRR6246951	12,631,260	638.4M	229.4Mb	2017-11-02

ID:: 4687424

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