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Antibody Fc-receptor common gamma chain FcεR1γ stabilizes cell surface receptors in group 3 innate lymphoid cells and promotes anti-infection immunity

GSE256409 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2024/06/05 Platform GPL21273Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 5 conditions, mostly with about 4 replicates eachGroups 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
Antibody Fc-receptor FcεR1γ stabilizes cell surface receptors in group 3 innate lymphoid cells and promotes anti-infection immunityNature communications · 2024
Summary (written by the submitters)
Group 3 innate lymphoid cells (ILC3s) are crucial for maintaining mucosal homeostasis and regulating inflammatory diseases, but the molecular mechanisms governing their phenotype and function are not fully understood. Here, we showed that ILC3s highly expressed Fcer1g gene, which encodes the antibody Fc-receptor common gamma chain (FcεR1γ).
Read the full summary ↓
Genetic perturbation of FcεR1γ led to the absence of critical cell membrane receptors NKp46 and CD16 in ILC3s. Alanine scanning mutagenesis identified two residues in FcεR1γ that stabilize its binding partners. FcεR1γ expression in ILC3s was essential for effective protective immunity against bacterial and fungal infections. Mechanistically, FcεR1γ influenced the transcriptional state and proinflammatory cytokine production of ILC3s, relying on the CD16-FcεR1γ signaling pathway. Overall, our findings highlight the significance of FcεR1γ as an adaptor protein that stabilizes cell membrane partners in ILC3s and promotes anti-infection immunity.
Published in
Antibody Fc-receptor FcεR1γ stabilizes cell surface receptors in group 3 innate lymphoid cells and promotes anti-infection immunity
Huang C, Zhu W, Li Q et al. · Nature communications 2024 · PMID 39013884 · doi:10.1038/s41467-024-50266-4
This dataset
Open GSE256409 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 GSE256409_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 PRJNA1079364 and SRA study SRP491114. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39013884) ↗
Study design
5 conditions, mostly with about 4 replicates each
WT ILC3, siLPs, PBS ×4 CKO ILC3, siLPs, infection ×4 CKO ILC3, cLPs, infection ×4 WT ILC3, siLPs, infection ×3 WT ILC3, cLPs, infection ×3 10x scRNAseq, HTO ×1 10x scRNAseq, 3' Gene Expression ×1

Supports a between-group comparison across 18 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 18 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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