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Series GSE85154 Query DataSets for GSE85154
Status Public on Aug 18, 2016
Title The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remain elusive. Here, we use a combination of genome-wide RNA-seq, ChIP-seq and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq, cytometry, and imaging analyses reveal functional compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes, and highlight transcriptional states beyond the current canonical classification. In addition, using antibiotic intervention and germ-free mice, we characterize the effect of the microbiome on the ILC regulatory landscape, and determine the response of ILCs to microbial colonization at the single-cell level. Together, our work characterizes the spectrum of transcriptional identities of small intestinal ILCs and describes how ILCs differentially integrate signals from the microbial microenvironment to generate phenotypic and functional plasticity.
Overall design ILC1(CD45+CD3-CD19-GR1-B220-CD127+RORγt-NkP46+), ILC2(CD45+CD3-CD19-GR1-B220-CD127+RORγt-KLRG1+) and ILC3(CD45+CD3-CD19-GR1-B220-CD127+RORγt+) were isolated from small intestine lamina propria of WT C57Bl/6 RORγt-GFP mice, or antibiotics treated mice (vancomycin, ampicillin,kanamycin, and metronidazole)
Contributor(s) Amit I
Citation(s) 27545347
Submission date Aug 03, 2016
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)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (24)
GSM2258610 Abx_ILC1_64
GSM2258611 Abx_ILC1_65
GSM2258612 WT_ILC1_B1T1
This SubSeries is part of SuperSeries:
GSE85157 The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome
BioProject PRJNA336451
SRA SRP080958

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
GSE85154_bulk_WT_Abx_homer.xlsx 3.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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