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Fecal microbiota transfer from autoimmune dry eye disease model mice to conventional mice induces ocular surface inflammation and stereotypic B cell receptor repertoire development in lacrimal gland

GSE263577 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/06/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 6 conditions, mostly with about 10 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
Gut microbiota transfer from autoimmune dry eye mice imprints stereotypic B cell receptor repertoires in the lacrimal gland and induces diseaseFrontiers in immunology · 2026
Summary (written by the submitters)
In this study, we transferred gut microbiota of SS-like autoimmune dry eye disease model mice to conventional B6 mice (NOD-FMT). After the transfer, NOD-FMT mice experienced a dramatic change in the gut microbiomes and showed clinicopathological features of SS, including increased corneal fluorescein staining score, decreased tear production, elevated levels of IL-6 mRNA, decreased levels of MUC5AC mRNA encoding mucin.
Read the full summary ↓
Additionally, we observed that NOD-FMT mice shared stereotypic B cell receptor (BCR) clonotypes with a much higher frequency compared to control group. B cell clones encoding these stereotypic BCR clonotypes developed and expanded locally in the lacrimal gland, and achieved systemic presence in certain clonotypes.
Published in
Gut microbiota transfer from autoimmune dry eye mice imprints stereotypic B cell receptor repertoires in the lacrimal gland and induces disease
Kim S, Lee S, Ju S et al. · Frontiers in immunology 2026 · PMID 42382782 · doi:10.3389/fimmu.2026.1827057
This dataset
Open GSE263577 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 GSE263577_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 PRJNA1098088 and SRA study SRP500590. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42382782) ↗
Study design
6 conditions, mostly with about 10 replicates each
C57BL/6, NOD-FMT, lacrimal gland, ×10 C57BL/6, NOD-FMT, spleen, ×10 C57BL/6, PBS-T, lacrimal gland, ×9 C57BL/6, PBS-T, spleen, ×9 C57BL/6, NC1, lacrimal gland, ×5 C57BL/6, NC1, spleen, ×5

Supports a between-group comparison across 48 samples.

How we read this: 6 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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