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Series GSE63338 Query DataSets for GSE63338
Status Public on Dec 05, 2014
Title Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ATAC-seq]
Organism Mus musculus
Experiment type Other
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 7 tissue-resident macrophage populations were isolated, as well as monocytes and neutrophils, and ATAC-seq (Assay for transposase-accessible chromatin using sequencing) was performed. Experiment was done in duplicates for all but Kupffer cells.
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 (17)
GSM1545943 MA_g04_ATAC_Microglia2
GSM1545944 MA_i7_ATAC_Spleen1
GSM1545945 MA_g05_ATAC_Lung1
This SubSeries is part of SuperSeries:
GSE63341 Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment
BioProject PRJNA267540
SRA SRP049940

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Supplementary file Size Download File type/resource
GSE63338_RAW.tar 559.7 Mb (http)(custom) TAR (of BIGWIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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