Genomics

Dataset Information

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Transcription profiling by high throughput sequencing of macrophages, monocytes, and neutrophils from fresh mouse tissues


ABSTRACT: 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 reprogrammed 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. 7 tissue-resident macrophage populations were isolated, as well as monocytes and neutrophils, and transcriptome analysis was performed. Experiment was done in duplicates.

REANALYSIS of: E-GEOD-63340

ORGANISM(S): Mus musculus  

PROVIDER: E-GEOD-63340 | ExpressionAtlas | 2016-09-23

REPOSITORIES: ExpressionAtlas

Dataset's files

Source:
Action DRS
E-GEOD-63340-analysis-methods.tsv Tabular
E-GEOD-63340-atlasExperimentSummary.Rdata Rdata
E-GEOD-63340-coexpressions.tsv.gz Tabular
E-GEOD-63340-configuration.xml Xml
E-GEOD-63340-factors.xml Xml
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Publications

Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment.

Lavin Yonit Y   Winter Deborah D   Blecher-Gonen Ronnie R   David Eyal E   Keren-Shaul Hadas H   Merad Miriam M   Jung Steffen S   Amit Ido I  

Cell 20141201 6


Macrophages are critical for innate immune defense and also control organ homeostasis in a tissue-specific manner. They provide a fitting model to study the impact of ontogeny and microenvironment on chromatin state and whether chromatin modifications contribute to macrophage identity. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have  ...[more]

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