GEO series

Decoding the Cell-Type and Spatial Roles of H19 in Cholestatic Liver Injury Through Single-Nucleus and Spatial Transcriptomics

GSE311100 Mus musculus (mouse) Spatial transcriptomics 13 samples Submitted 2026/04/30 Platform GPL24247Platform GPL30172

At a glance

Spatial transcriptomics · mouse · 13 samples

What it is: Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism: Mus musculus (mouse)
Samples: 13 samples: 4 × Liver, DKO, GeoMx, vs 4 × Liver, Mdr2KO, GeoMx,Groups 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: Decoding the role of H19 in cholestatic liver injury using snRNA-seq, spatial transcriptomics, and machine learning-based disease predictionCell & bioscience · 2026

Summary (written by the submitters)

Despite recent advances, Primary Sclerosing Cholangitis (PSC)-a chronic obstructive biliary disease-still lacks effective therapies to prevent disease progression or the need for liver transplantation. Long non-coding RNA H19 (H19) has been implicated in promoting PSC disease progression. However, the underlying cell-specific and molecular mechanisms by which H19 contributes to PSC pathogenesis remain incompletely understood.

Read the full summary ↓

Here we used single nucleus RNA sequencing (snRNAseq) and spatial transcriptomics to elucidate the cell- and spatial-specific expression alterations associated with H19 in the Mdr2KO PSC mouse model.

Published in

Decoding the role of H19 in cholestatic liver injury using snRNA-seq, spatial transcriptomics, and machine learning-based disease prediction

Way GW, Jiang X, Lu H et al. · Cell & bioscience 2026 · PMID 42216109 · doi:10.1186/s13578-026-01590-3

This dataset

Open GSE311100 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 GSE311100_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1368669 and SRA study SRP648356. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42216109) ↗

Study design

4 × Liver, DKO, GeoMx, vs 4 × Liver, Mdr2KO, GeoMx,

Supports a between-group comparison across 8 samples.

How we read this: 2 replicated groups read from 13 sample titles; they account for 8 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

GSM9316928 Liver, WT, snRNAseq, HZ4978
GSM9316929 Liver, H19KO, snRNAseq, HZ4979
GSM9316930 Liver, Mdr2KO, snRNAseq, HZ4980
GSM9316931 Liver, DKO, snRNAseq, HZ4981
GSM9316932 Liver, DKO, GeoMx, 5712 Liver, DKO, GeoMx,
GSM9316933 Liver, DKO, GeoMx, 5713 Liver, DKO, GeoMx,
GSM9316934 Liver, DKO, GeoMx, 5714 Liver, DKO, GeoMx,
GSM9316935 Liver, DKO, GeoMx, 5715 Liver, DKO, GeoMx,
GSM9316936 Liver, Mdr2KO, GeoMx, 5850 Liver, Mdr2KO, GeoMx,
GSM9316937 Liver, Mdr2KO, GeoMx, 5851 Liver, Mdr2KO, GeoMx,
GSM9316938 Liver, Mdr2KO, GeoMx, 5852 Liver, Mdr2KO, GeoMx,
GSM9316939 Liver, Mdr2KO, GeoMx, 5853 Liver, Mdr2KO, GeoMx,
GSM9316940 Negative Control

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