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| 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.
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| 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)
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| |
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| Contributor(s) |
Amit I |
| Citation(s) |
27545347 |
| Submission date |
Aug 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| 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)
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| This SubSeries is part of SuperSeries: |
| GSE85157 |
The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome |
|
| Relations |
| BioProject |
PRJNA336451 |
| SRA |
SRP080958 |
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