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Single-cell transcriptomic gene regulatory network analysis uncovers the alteration of colonic stem and immune cell homeostasis in Nr4a1 knockout mice

GSE306798 Mus musculus (mouse) Single-cell RNA-seq 8 samples Submitted 2026/07/07 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 8 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
8 samples: 4 × Mouse, NR4A1 KO, colon tissue, vs 4 × Mouse, wild type, colon tissue,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.
Summary (written by the submitters)
Recent findings suggest that the orphan nuclear receptor 4A (NR4A) can regulate cellular energetics and epithelial defenses, contributing to a resilient disease resistant phenotype. However, its role in regulating intestinal crypt homeostasis remains unclear. To assess the effects of NR4A on intestinal epithelial, stromal and immune cell heterogeneity and functional phenotypes, we utilized single-cell transcriptomics and advanced analytic strategies to generate a high-quality atlas for the colonic epithelium from wild-type and whole body Nr4a1 knockout mice.
Read the full summary ↓
Here we observed a widespread effect of Nr4a1 deletion on intercellular communication involving intestinal stem cells, macrophages, T and B cells, and fibroblasts, indicating a complex and pervasive remodeling of the colonic epithelial and immune microenvironments and their regulatory networks. This alteration in cell-cell crosstalk was associated with an elevated single-cell entropy, indicative of higher differentiation potential and stem-like properties in epithelial, stromal and immune cell types. Our work provides new evidence of the molecular function of Nr4a1 as a critical regulatory factor in stem cell and immune homeostasis in the colon.
This dataset
Open GSE306798 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 GSE306798_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 PRJNA1312366 and SRA study SRP614522. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × Mouse, NR4A1 KO, colon tissue, vs 4 × Mouse, wild type, colon tissue,

Supports a between-group comparison across 8 samples.

How we read this: 2 replicated groups read from 8 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
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.