GEO series

Single-cell transcriptomics of spinal microglia from Cx3cr1-Cre-YFP x flxRunx1 mice

GSE123064 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2026/01/30 Platform GPL21103

At a glance

Single-cell RNA-seq · mouse · 2 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: 2 samples
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: Runx1 transcription factor modulates opioid analgesia and withdrawal in humans and rodentsNeuron · 2026

Summary (written by the submitters)

Runx1 is a transcription factor known to be involved in microglial reactivity in the perinatal period, but its role in regulating microglia reactivity later in life is not well understood. Transgenic mice with a conditional inducible deletion of the transcription factor Runx1 in Cx3cr1 positive cells were generated to further investigate.

Read the full summary ↓

Immunohistochemical labelling and electron microscopy, flow cytometry and quantitative PCR showed indications of altered microglial phenotype in knock-out mice. Single-cell seq was pursused to further delineate the microglial populations in wild-type and Runx1 knock-out mice.

Published in

Runx1 transcription factor modulates opioid analgesia and withdrawal in humans and rodents

Leduc-Pessah H, McAllister BB, Sinha S et al. · Neuron 2026 · PMID 41619726 · doi:10.1016/j.neuron.2025.11.018

This dataset

Open GSE123064 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 GSE123064_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 PRJNA507432 and SRA study SRP171124. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41619726) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

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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.