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Series GSE89646 Query DataSets for GSE89646
Status Public on Nov 28, 2016
Title Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes
Organism Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used ATAC-seq to define chromatin accessibility in predicted enhancer regions of intestinal αβ+ and γδ+ intraepithelial lymphocytes (IELs) purified from germ-free mice, their conventionally-raised (CONV-R) counterparts, and mice reared GF and then colonized with a CONV-R gut microbiota at the end of the suckling-weaning transition. Characterizing genes adjacent to traditional enhancers and super-enhancers revealed signaling networks, metabolic pathways, and enhancer-associated transcription factors affected by the microbiota. Our results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.
Overall design We interrogated chromatin accessibility using ATAC-seq in four cell types derived from mice (CD4+ T cells, CD8+ T cells, αβ+ intraepithelial lymphocytes, and γδ+ intraepithelial lymphocytes), across three gut microbial colonization states (germ-free, conventionally-raised, and conventionalized).
Contributor(s) Gordon JI, Semenkovich NP
Citation(s) 27911843
Submission date Nov 08, 2016
Last update date May 15, 2019
Contact name Jeffrey Gordon
Organization name Washington University
Department Center for Genome Sciences & Systems Biology
Street address 4515 McKinley Research Building
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (91)
GSM2385967 GF.1 TCR αβ+ IEL
GSM2385968 GF.1 TCR γδ+ IEL
GSM2385969 GF.1 CD4+ T cell
BioProject PRJNA352791
SRA SRP092893

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Supplementary file Size Download File type/resource
GSE89646_RAW.tar 18.9 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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