GEO series

Single-cell RNA sequencing of peripheral blood and brain immune cells in mouse models of ischemic stroke

GSE343642 Mus musculus (mouse) Single-cell RNA-seq 8 samples Submitted 2026/08/19 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 8 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: 8 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.

Summary (written by the submitters)

Ischemic stroke induces profound alterations in peripheral and brain immune responses, but the cellular and transcriptional heterogeneity underlying these responses remains incompletely understood. To characterize immune-cell populations and their transcriptional states under different experimental conditions, we performed single-cell RNA sequencing of immune cells from mice.

Read the full summary ↓

Single-cell RNA sequencing was performed on immune cells under different experimental conditions, as well as peripheral blood and brain immune cells from mice subjected to middle cerebral artery occlusion (MCAO), including mice with and without hemorrhagic transformation (HT). These datasets provide a resource for investigating immune-cell heterogeneity and transcriptional responses associated with ischemic stroke.

This dataset

Open GSE343642 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 GSE343642_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 PRJNA1512045 and SRA study SRP726681. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 8 more — browse all 8 samples with per-sample file links →

Datasets on a similar topic

GSE225948 Brain and blood single-cell transcriptomic analysis in acute and subacute phases after experimental stroke 29 samples shares single-cell, stroke, blood, brain
GSE319238 Single-cell transcriptomic analysis of microglia and brain cells after ischemic stroke 12 samples shares single-cell, ischemic, stroke, brain
GSE326055 Single-cell RNA sequencing reveals blood contact-dependent functional specialization of vascular-associated immune cells in a MCAO model 4 samples shares single-cell, blood
GSE302808 Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain Injury 84 samples shares peripheral, brain
GSE269748 A single-cell atlas deconstructs heterogeneity across multiple models in murine traumatic brain injury and identifies novel cell-specific targets 36 samples shares single-cell, brain
GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares ischemic, stroke
GSE319237 Transcriptomic profiling of mouse microglia after ischemic stroke 15 samples shares ischemic, stroke
GSE280862 Loss of Sarm1 Mitigates Axonal Degeneration and Promotes Neuronal Regeneration After Ischemic Stroke 15 samples shares ischemic, stroke

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.