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Series GSE176148 Query DataSets for GSE176148
Status Public on Dec 22, 2021
Title H3K27me3 Cut&Tag profiling of bone marrow-derived alveolar macrophages from wildtype and Suz12 knockout mice
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Macrophages are at the forefront of immune responses and their transcriptional programs are modified by their tissue environment and in response to immunological challenge. Post-translational modifications of histones, such as histone H3 lysine 27 tri-methylation (H3K27me3) by the polycomb repressive complex 2 (PRC2), are tightly associated with epigenetic regulation of gene expression. To explore whether H3K27me3 is involved in either the establishment or function of the mononuclear phagocyte system, we selectively deleted the SUZ12 gene in mice, a core component of PRC2. Consistent with the the role of PRC2 in maintaining transcriptional repression, we found that the majority of top-ranked genes enriched for H3K27me3 in wild type alveolar macrophages were upregulated in SUZ12 knock-out alveolar macrophages.
 
Overall design C57BL/6-Ly5.1 mice were lethally irradiated and reconstituted with either a ratio of 90% wt Ly5.2: 10% wt Ly5.1, or 90% Suz12 cKO Ly5.2: 10% wt ly5.1. Libraries were generated from 100,000 alveolar macrophages sorted from the lung of wt (2 biological replicates) or Suz12cKO mice (2 biological replicates). Samples were sequenced with an Illumina NextSeq platform, producing between 5-8 million paired-end 36bp reads per sample.
 
Contributor(s) Baldoni PL, Smyth GK
Citation(s) 34533976
Submission date Jun 04, 2021
Last update date Dec 24, 2021
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM5357022 H3k27me3-ko-1
GSM5357023 H3k27me3-ko-2
GSM5357024 H3k27me3-WT-1
This SubSeries is part of SuperSeries:
GSE176117 RNA-seq profiling of bone marrow-derived alveolar macrophages, foetal-derived alveolar macrophages and foetal-derived Langerhans cells from the lungs of wildtype and Suz12 knockout mice
Relations
BioProject PRJNA735134
SRA SRP322710

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE176148_GenewiseCounts.tsv.gz 276.8 Kb (ftp)(http) TSV
GSE176148_RAW.tar 750.0 Kb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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