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The long noncoding RNA lnc13 restrains inflammatory responses to maintain oral tolerance to gluten

GSE298129 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/03/04 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 15 conditions, mostly in duplicateGroups 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
The long noncoding RNA lnc13 restrains inflammatory responses to maintain oral tolerance to glutenNature immunology · 2026
Summary (written by the submitters)
Celiac disease (CeD) is an autoimmune disorder triggered by dietary gluten. While HLA-DQ2/8-mediated presentation of gliadin peptides is required for disease, the mechanisms that underlie the loss of oral tolerance to gluten remain incompletely understood. Long noncoding RNAs (lncRNAs) have been increasingly recognized as regulators of immune function, yet their role in oral tolerance has not been previously explored.
Read the full summary ↓
Using a screen designed to identify lncRNAs responsive to T cell activation and enriched for CeD-associated GWAS variants, we identified lnc13 as a top candidate. In HLA-DQ8 transgenic mice lacking lnc13, unmanipulated gluten ingestion led to hallmark features of loss of oral tolerance to gluten: reduced regulatory T cells, and increased IFN-γ⁺ lymphocytes, IL-12⁺ myeloid cells, cytotoxic intraepithelial immune cells and crypt hyperplasia in the small intestine. Mechanistically, lnc13 binds specific DNA regulatory regions and limits inflammatory responses to pro-inflammatory signals. In particular, lnc13 restrains IL-15-driven differentiation of CD8⁺ NK-like lymphokine-activated killer cells—an IL-15–dependent pathway strongly implicated in CeD. These findings establish lnc13 as a critical noncoding modulator of oral gluten tolerance.
Published in
The long noncoding RNA lnc13 restrains inflammatory responses to maintain oral tolerance to gluten
Yang-Fischer R, Shearer A, Leão FB et al. · Nature immunology 2026 · PMID 42062562 · doi:10.1038/s41590-026-02506-6
This dataset
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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 GSE298129_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 PRJNA1268408 and SRA study SRP588459. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42062562) ↗
Study design
15 conditions, mostly in duplicate
lnc13-WT-DQ8 CD8ab IEL biol ×3 lnc13-KO-DQ8 CD8ab IEL biol ×3 lnc13-WT CD8 IL15-biol ×3 lnc13-KO CD8 IL15-biol ×3 lnc13-WT CD8 unstim-biol ×3 lnc13-KO CD8 unstim-biol ×3 lnc13-WT-DQ8 tissue-biol ×2 lnc13-KO-DQ8 tissue-biol ×2 +7 more

Supports a between-group comparison across 36 samples.

How we read this: 15 replicated groups read from 36 sample titles; they account for 36 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
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