GEO series

An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [scRNA-seq]

GSE280985 Mus musculus (mouse) Single-cell RNA-seq 14 samples Submitted 2026/02/17 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 14 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitisNature communications · 2026

Summary (written by the submitters)

The liver biliary niche serves as a reservoir of tissue-resident immune cells and supports tissue fibrosis upon damage, yet the role of peribiliary immune cells during cholangitis remains poorly understood. Here, we induce cholestatic liver injury mirroring human biliary diseases with bile acid retention in mice to establish a spatial and multimodal single-cell RNA sequencing atlas of the liver and liver-draining lymph nodes (LN).

Read the full summary ↓

We characterized a hepatic disease state trajectory from dendritic cell precursors (preDCs) to a mature subset of pro-inflammatory Mgl2+ type 2 conventional dendritic cells (cDC2B) and observed dynamic crosstalk with γδ T cells inducing an Il17 response (γδ T17). Dissection of the cDC2B-γδ T cell communication node identified the Icosl-Icos pair as an important cell contact-dependent interaction, which was validated in vitro. In vivo, cDC2B depletion attenuated γδ T17 responses in cholestatic liver injury, and liver fibrosis was reduced in a model of inducible γδ T cell depletion and in an Il17-deficient background. Our work demonstrates dynamic turnover of cDC2 within the biliary niche during cholestasis, and a profibrogenic function of γδ T cells contingent on the induction by peribiliary cDC2B, highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche.

Published in

An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis

Thomann S, Hemmer H, Agrawal A et al. · Nature communications 2026 · PMID 41963321 · doi:10.1038/s41467-026-71537-2

This dataset

Open GSE280985 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 GSE280985_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1181780 and SRA study SRP543324. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41963321) ↗

Study design

14 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. 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

GSM8608379 mouse, liver, D0, protocol A
GSM8608380 mouse, liver, D0, protocol B
GSM8608381 mouse, liver, D3, protocol A
GSM8608382 mouse, liver, D3, protocol B
GSM8608383 mouse, liver, D5, protocol A
GSM8608384 mouse, liver, D5, protocol B
GSM8608385 mouse, liver, D9, protocol A
GSM8608386 mouse, liver, D9, protocol B
GSM8608387 mouse, liver, D19, protocol A
GSM8608388 mouse, liver, D19, protocol B
GSM8608389 mouse, liver, D25, protocol A
GSM8608390 mouse, liver, D25, protocol B
GSM8608391 mouse liver STOP
GSM8608392 mouse liver, D5-DT

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