GEO series

The neuropeptide Neuromedin U stimulates innate lymphoid cells and promotes type 2 inflammation [ILC2 and ILC3]

GSE101623 Mus musculus (mouse) RNA-seq (gene expression) 6 samples Submitted 2017/08/18 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 6 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 6 samples: 3 × ILC2_SI_SPF vs 3 × ILC3_SI_SPFGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

The type 2 cytokines interleukin (IL)-4, IL-5, IL-9 and IL-13 play critical roles in stimulating innate and adaptive immune responses required for resistance to helminth infection and promotion of allergic inflammation, metabolic homeostasis and tissue repair. Group 2 innate lymphoid cells (ILC2s) are a potent source of type 2 cytokines and while significant advances have been made in understanding the cytokine milieu that promotes ILC2 responses, there are fundamental gaps in knowledge regarding how ILC2 responses are regulated by other stimuli.

Read the full summary ↓

In this report, we demonstrate that ILC2s in the gastrointestinal tract co-localize with cholinergic neurons that express the neuropeptide neuromedin U (NMU). In contrast to other hematopoietic cells, ILC2s selectively express the NMU receptor 1 (NMUR1). In vitro stimulation of ILC2s with NMU induced rapid cell activation, proliferation and secretion of type 2 cytokines IL-5, IL-9 and IL-13 that was dependent on cell-intrinsic expression of NMUR1 and Gaq protein. In vivo administration of NMU triggered potent type 2 cytokine responses characterized by ILC2 activation, proliferation and eosinophil recruitment that was associated with accelerated expulsion of the gastrointestinal nematode Nippostrongylus brasiliensis or induction of lung inflammation. Conversely, worm burden was higher in Nmur1-/- mice compared to control mice. Further, use of gene-deficient mice and adoptive cell transfer experiments revealed that ILC2s were necessary and sufficient to mount NMU-elicited type 2 cytokine responses. Together, these data indicate that the NMU-NMUR1 neuronal signaling circuit provides a selective and previously unrecognized mechanism through which the enteric nervous system and innate immune system integrate to promote rapid type 2 cytokine responses that can induce anti-microbial, inflammatory and tissue-protective type 2 responses at mucosal sites.

This dataset

Open GSE101623 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE101623_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA395027 and SRA study SRP112885. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28869965) ↗

Study design

3 × ILC2_SI_SPF vs 3 × ILC3_SI_SPF

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 6 sample titles; they account for 6 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM2711098 ILC2_SI_SPF1 ILC2_SI_SPF
GSM2711099 ILC2_SI_SPF2 ILC2_SI_SPF
GSM2711100 ILC2_SI_SPF3 ILC2_SI_SPF
GSM2711101 ILC3_SI_SPF1 ILC3_SI_SPF
GSM2711102 ILC3_SI_SPF2 ILC3_SI_SPF
GSM2711103 ILC3_SI_SPF3 ILC3_SI_SPF

Datasets on a similar topic

GSE101625 The neuropeptide Neuromedin U stimulates innate lymphoid cells and promotes type 2 inflammation 13 samples shares neuropeptide, neuromedin, stimulates, lymphoid, promotes, innate
GSE101624 The neuropeptide Neuromedin U stimulates innate lymphoid cells and promotes type 2 inflammation [NMU] 7 samples shares neuropeptide, neuromedin, stimulates, lymphoid, promotes, innate
GSE271362 CGRP-Related Neuropeptide Adrenomedullin 2 Promotes Tissue-Protective ILC2 Responses and Limits Intestinal Inflammation 11 samples shares ilc2, neuropeptide, promotes
GSE73272 RNA-Seq analysis of mouse group 2 innate lymphoid cells (ILC2s) cultured with IL-33, IFN-g, and IL-27 9 samples shares ilc2, lymphoid, innate
GSE102299 Neuromedin U receptor-1 amplifies inflammatory lung innate lymphoid cells 770 samples shares neuromedin, lymphoid, innate
GSE275251 Pulmonary fibroblast-derived stem cell factor promotes neutrophilic asthma by augmenting IL-17A production from ILC3s 8 samples shares ilc3, promotes
GSE288754 Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis [ILC3s bulk RNA-seq] 6 samples shares ilc3, promotes
GSE288751 Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis [scRNA-seq] 4 samples shares ilc3, promotes

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.