GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE63339 Query DataSets for GSE63339
Status Public on Dec 05, 2014
Title Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Macrophages are hematopoietic cells critical for innate immune defense, but also control organ homeostasis in a tissue-specific manner. Tissue-resident macrophages, therefore, provide a well-defined model to study the impact of ontogeny and microenvironment on chromatin state. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations, as well as monocytes and neutrophils. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have distinct enhancer landscapes. Our work suggests that a combination of tissue and lineage-specific transcription factors form the regulatory networks controlling chromatin specification in tissue-resident macrophages. The environment has the capacity to alter the chromatin landscape of macrophages derived from transplanted adult bone marrow in vivo and even differentiated macrophages are reprogramed when transferred into a new tissue. Altogether, these data provide a comprehensive view of macrophage regulation and highlight the importance of microenvironment along with pioneer factors in orchestrating macrophage identity and plasticity.
Overall design indicated cells were cross-linked and sorted, then ChIP-seq was performed with the indicated antibody. For chimera samples - CD45.2 mice were irradiated, bone marrow from CD45.1 mice was then transplanted. 4 months later, CD45.1 macrophages were isolated from the indicated tissues, and ChIP-seq was performed.
Citation(s) 25480296
Submission date Nov 17, 2014
Last update date May 15, 2019
Contact name Ido Amit
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (80)
GSM1545960 Microglia_K4Me1_rep1
GSM1545961 Microglia_K27Ac_rep1
GSM1545962 Microglia_K4Me1_rep2
This SubSeries is part of SuperSeries:
GSE63341 Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment
BioProject PRJNA267541
SRA SRP049941

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
GSE63339_RAW.tar 7.8 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap