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Series GSE62826 Query DataSets for GSE62826
Status Public on Dec 04, 2014
Title Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Macrophages reside in essentially all tissues of the body and play key roles in innate and adaptive immune responses. Distinct populations of tissue macrophages also acquire context-specific functions that are important for normal tissue homeostasis. To investigate mechanisms responsible for tissue-specific functions, we analyzed the transcriptomes and enhancer landscapes of brain microglia and resident macrophages of the peritoneal cavity. In addition, we exploited natural genetic variation as a genome-wide “mutagenesis” strategy to identify DNA recognition motifs for transcription factors that promote common or subset-specific binding of the macrophage lineage-determining factor PU.1. We find that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers. These findings provide insights into molecular mechanisms by which tissue environment influences macrophage phenotypes that are likely to be broadly applicable to other cell types.
 
Overall design Chromatin marks H3K4me2, H3K27Ac, and transcription factors PU.1 were assessed by ChIP-Seq and RNA-Seq were used to measure gene expression in 5 different macrophage subtypes.
 
Contributor(s) Glass CK
Citation(s) 25480297
Submission date Oct 29, 2014
Last update date May 15, 2019
Contact name David Gosselin
E-mail(s) dgosselin@ucsd.edu
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (86)
GSM1533885 BMDM H3K27Ac ChIP-Seq C57BL6/J no treatment
GSM1533886 BMDM H3K4me2 ChIP-Seq C57BL6/J no treatment
GSM1533887 BMDM Input DNA for Mnase ChIP-Seq C57BL6/J no treatment
Relations
BioProject PRJNA265386
SRA SRP049388

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
GSE62826_GeneExpressionPolyA.txt.gz 1.9 Mb (ftp)(http) TXT
GSE62826_GeneExpressionReplicates.txt.gz 1.9 Mb (ftp)(http) TXT
GSE62826_GeneExpressionRiboZero.txt.gz 2.3 Mb (ftp)(http) TXT
GSE62826_GeneExpressionStrains.txt.gz 1.8 Mb (ftp)(http) TXT
GSE62826_RAW.tar 11.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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