GEO series

Spatial organization, chromatin accessibility and gene-regulatory programs defining sensory neurons

GSE287551 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/04/10 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 10 samples: 10 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: Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neuronsCommunications biology · 2025

Summary (written by the submitters)

Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity.

Read the full summary ↓

Here, we generated an integrated atlas from high-quality scRNA-seq datasets of the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirmed cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We generated a cell type specific open chromatin atlas that revealed enhancer driven regulons and gene-regulatory networks. These were organized into co-regulated gene-programs that together defined sensory neuron diversity. Cell type complexity was found to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.

Published in

Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons

Krauter D, Kupari J, Usoskin D et al. · Communications biology 2025 · PMID 40500276 · doi:10.1038/s42003-025-08315-1

This dataset

Open GSE287551 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 GSE287551_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1213725 and SRA study SRP558699. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40500276) ↗

Study design

10 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 10 sample titles: 10 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

GSM8747643 Multiome, DRG neurons, wild-type1 GEX
GSM8747644 Multiome, DRG neurons, wild-type1 ATAC
GSM8747645 Multiome, DRG neurons, wild-type2 GEX
GSM8747646 Multiome, DRG neurons, wild-type2 ATAC
GSM8747647 Multiome, DRG neurons, wild-type3 GEX
GSM8747648 Multiome, DRG neurons, wild-type3 ATAC
GSM8747649 Multiome, DRG neurons, wild-type4 GEX
GSM8747650 Multiome, DRG neurons, wild-type4 ATAC
GSM8747651 Multiome, DRG neurons, wild-type5 GEX
GSM8747652 Multiome, DRG neurons, wild-type5 ATAC

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Search all mouse RNA-seq datasets in GEO →

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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.