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Single Cell Sequencing Data of Mouse Spinal Cord with Dorsal Column Lesion and Astrocyte-Specific Ryk conditional Knockout

GSE205029 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2025/03/28 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 16 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
16 samples: 16 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
Astrocytic Ryk signaling coordinates scarring and wound healing after spinal cord injuryProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
After the data quality control, a total of 18,203 captured cells were subjected to clustering analysis by leiden and visualized in lower dimension by uniform manifold approximation and projection (UMAP). The results showed that they could be clustered into 17 distinct cell clusters.
Read the full summary ↓
According to the highest differentially expressed genes (DEGs) and canonical markers used in prior studies, we annotated these 17 clusters as 13 major cell types with distinct expression profiles): Astrocytes (ASC, containing 3 clusters: Astro_2, Astro_5, and Astro_7), microglia (MG, containing 2 clusters: Microglial_6 and Microglial_10), oligodendrocytes (containing 2 clusters: Oligo_4 and Oligo_8), endothelial cells (containing 1 cluster: Endothelial_1), pericytes (Pericytes_9), fibroblasts (Fibroblasts_14), neuronal cells (Neuronal_3), oligodendrocyte progenitor cells (OPC_11), Schwann cells (schwan cells_15), red blood cells (RBC_17), immune cells (Immuno_12), myeloid cells (myeloid Cells_16)
Published in
Astrocytic Ryk signaling coordinates scarring and wound healing after spinal cord injury
Shen Z, Feng B, Lim WL et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40208942 · doi:10.1073/pnas.2417400122
This dataset
Open GSE205029 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 GSE205029_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 PRJNA843115. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40208942) ↗
Study design
16 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 16 sample titles: 16 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
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.