GEO series

Anatomical diversity of the adult corticospinal tract revealed by single cell transcriptional profiling.

GSE293184 Mus musculus (mouse) Single-cell RNA-seq 15 samples Submitted 2026/03/25 Platform GPL17021

At a glance

Single-cell RNA-seq · mouse · 15 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: 15 samples: 5 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.
Paper: Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional ProfilingThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2023

Summary (written by the submitters)

The corticospinal tract (CST) forms a central part of the voluntary motor apparatus in all mammals. Thus, injury, disease, and subsequent degeneration within this pathway result in chronic irreversible functional deficits. Current strategies to repair the damaged CST are sub-optimal in part due to underexplored molecular heterogeneity within the adult tract.

Read the full summary ↓

Here we combine spinal retrograde CST tracing with single-cell RNA sequencing in adult male and female mice to index corticospinal neuron (CSN) subtypes that differentially innervate the forelimb and hindlimb. We exploit publicly available datasets to confer anatomical specialization among CSNs and show that CSNs segregate not only along the forelimb and hindlimb axis but also by supraspinal axon collateralization. These anatomically defined transcriptional data allow us to use machine learning tools to build classifiers that discriminate between CSNs and cortical layer 2/3 and non-spinally terminating layer 5 neurons in M1, and separately identify limb specific CSNs. Utilizing these tools, CSN subtypes can be differentially identified to study postnatal patterning of the CST in vivo, leveraged to screen for novel limb-specific axon growth survival and growth activators in vitro, and ultimately exploited to repair the damaged CST after injury and disease.

Published in

Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling

Golan N, Ehrlich D, Bonanno J et al. · The Journal of neuroscience : the official journal of the Society for Neuroscience 2023 · PMID 37748862 · doi:10.1523/JNEUROSCI.0811-22.2023

This dataset

Open GSE293184 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 GSE293184_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 PRJNA1243315 and SRA study SRP573874. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37748862) ↗

Study design

5 conditions, mostly in triplicate

Forelimb CSNs, layer 5 M1, ×3 Forelimb non-CSNs, layer 5 M1, ×3 Hind limb CSNs, layer 5 M1, ×3 Hind limb non-CSNs, layer 5 M1, ×3 Ai14+ CSNs, layer 5 M ×2 Ai14- non-CSNs, layer 5 M ×1

Supports a between-group comparison across 14 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 14 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

GSM8878088 Forelimb CSNs, layer 5 M1, replicate 1 Forelimb CSNs, layer 5 …
GSM8878089 Forelimb non-CSNs, layer 5 M1, replicate 1 Forelimb non-CSNs, laye…
GSM8878090 Forelimb CSNs, layer 5 M1, replicate 2 Forelimb CSNs, layer 5 …
GSM8878091 Forelimb non-CSNs, layer 5 M1, replicate 2 Forelimb non-CSNs, laye…
GSM8878092 Forelimb CSNs, layer 5 M1, replicate 3 Forelimb CSNs, layer 5 …
GSM8878093 Forelimb non-CSNs, layer 5 M1, replicate 3 Forelimb non-CSNs, laye…
GSM8878094 Hind limb CSNs, layer 5 M1, replicate 1 Hind limb CSNs, layer 5…
GSM8878095 Hind limb non-CSNs, layer 5 M1, replicate 1 Hind limb non-CSNs, lay…
GSM8878096 Hind limb CSNs, layer 5 M1, replicate 2 Hind limb CSNs, layer 5…
GSM8878097 Hind limb non-CSNs, layer 5 M1, replicate 2 Hind limb non-CSNs, lay…
GSM8878098 Hind limb CSNs, layer 5 M1, replicate 3 Hind limb CSNs, layer 5…
GSM8878099 Hind limb non-CSNs, layer 5 M1, replicate 3 Hind limb non-CSNs, lay…
GSM8878100 Forelimb rbp4-cre:Ai14+ CSNs, layer 5 M1 Ai14+ CSNs, layer 5 M
GSM8878101 Forelimb and hindlimb rbp4-cre:Ai14- non-CSNs, layer 5 M1
GSM8878102 Hind limb rbp4-cre:Ai14+ CSNs, layer 5 M1 Ai14+ CSNs, layer 5 M

Datasets on a similar topic

GSE283143 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the proximal to distal transcriptome 36 samples shares anatomical, diversity
GSE283495 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the global transcriptome 29 samples shares anatomical, diversity
GSE283142 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the crypt/villus transcriptome 24 samples shares anatomical, diversity
GSE297572 Innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by bulk RNA-seq 22 samples shares revealed, tract
GSE308576 Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons. 6 samples shares corticospinal, tract
GSE313126 Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons [snRNA-Seq] 4 samples shares corticospinal, tract
GSE263902 The translational landscape of mouse oocytes and preimplantation embryos revealed by high-resolution ribosome profiling 272 samples shares revealed
GSE215959 Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [M4_aCTLA4_scRNA] 1248 samples shares revealed

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.