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Deep Cellular and Spatial Profiling of the Mouse Spinal Cord Reveals Sex-Specific Neuron Types and the Ascending Projection Neuron Repertoire

GSE318731 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 72 samples Submitted 2026/02/16 Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 72 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
72 samples: 24 conditions, mostly in triplicateGroups 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)
Spinal cord gives rise to central somatosensation and orchestrates autonomic and motor control. How its cellular diversity achieves physiological functions across sex and along its longitudinal axis and links spinal cord to higher order brain centers remains poorly understood. Here we used retrograde viral tracing with spatial transcriptomics and multiomic profiling of >750k mouse spinal cord neurons to define its output logic and functional cellular repertoire.
Read the full summary ↓
We identified 70 spinal projection neuron classes that link the spinal cord to hind-, mid-, and forebrain centers implicated in itch, touch, and pain revealing the output wiring logic of the spinal cord. Furthermore, we characterized >500 anatomically and transcriptomically distinct neuron types that revealed extensive (~50%) rostro-caudal cellular specialization as well as first sex specific neuron classes in the spinal cord. Finally, we assembled a neuron-class-to-phenotype map of the structure based on genetically defined interventions. As a result, we deliver an anatomically and functionally annotated cellular atlas of the complete adult mouse spinal cord to guide future interrogation of the organ.
This dataset
Open GSE318731 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 GSE318731_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 PRJNA1419852 and SRA study SRP675329. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
24 conditions, mostly in triplicate
Mouse cervical spinal cord snRNA-seq_biol_rep… ×3 Mouse cervical spinal cord snATAC-seq_biol_re… ×3 Mouse cervical spinal cord snRNA-seq_biol_rep… ×3 Mouse cervical spinal cord snATAC-seq_biol_re… ×3 Mouse cervical spinal cord snRNA-seq_biol_rep… ×3 Mouse cervical spinal cord snATAC-seq_biol_re… ×3 Mouse thoracic spinal cord snRNA-seq_biol_rep… ×3 Mouse thoracic spinal cord snATAC-seq_biol_re… ×3 +16 more

Supports a between-group comparison across 72 samples.

How we read this: 24 replicated groups read from 72 sample titles; they account for 72 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

+ 32 more — browse all 72 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.