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ILC2-derived LIF licences progression from tissue-localized to systemic immunity

GSE243691 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2024/07/30 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 8 conditions, mostly in triplicateGroups 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.
Paper
ILC2-derived LIF licences progress from tissue to systemic immunityNature · 2024
Summary (written by the submitters)
Migration and homing of immune cells are critical for immune surveillance. Efficient trafficking is mediated by cellular expression of combinations of adhesion and chemokine receptors which guide immune cells, in response to chemokine signals, to specific locations within tissues and the lymphatic system. This supports tissue-localized immune reactions and systemic immunity.
Read the full summary ↓
However, fundamental questions remain as to how these signals are initiated and regulated. Here we show that disruption of leukaemia inhibitory factor (LIF) production from group 2 innate lymphoid cells (ILC2s) prevents immune cells from leaving the lungs and migrating to the lymph nodes. During pulmonary viral infection this dysregulation leads to plasmacytoid dendritic cells becoming retained in the lungs where they improve tissue-localized anti-viral immunity. By comparison, during chronic allergen challenge the accumulation of immune cells in the lung leads to the pronounced formation of tertiary lymphoid structures in the lung, and a failure to seed the lymph nodes. Mechanistically, ILC2-derived LIF induces the production of the chemokine CCL21 from lymphatic endothelial cells lining the pulmonary lymphatic vessels, thereby licencing the homing of CCR7+ immune cells to lymph nodes. Thus, ILC2-derived LIF production dictates the egress of immune cells from the lungs regulating tissue versus systemic immunity and the balance between allergen and viral responsiveness in the lungs.
Published in
ILC2-derived LIF licences progress from tissue to systemic immunity
Gogoi M, Clark PA, Ferreira ACF et al. · Nature 2024 · PMID 39112698 · doi:10.1038/s41586-024-07746-w
This dataset
Open GSE243691 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 GSE243691_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 PRJNA1019393 and SRA study SRP462110. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39112698) ↗
Study design
8 conditions, mostly in triplicate
pDC_PBS ×5 ILC2_PBS ×5 pDC_IL33 ×4 ILC2 LN ×3 ILC2 Lung ×3 ILC2 LP ×3 ILC2 FAT ×3 ILC2p ×2

Supports a between-group comparison across 28 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 28 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
Datasets on a similar topic

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