Single-cell transcriptomic analysis of microglia and brain cells after ischemic stroke
Single-cell RNA-seq · mouse · 12 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
- 12 samples: 12 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE319238_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1422658 and SRA study SRP676496. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM9514178 scRNA-seq of mouse microglia, sham surgery, wild-type
- GSM9514179 scRNA-seq of mouse microglia, MCAO Day 14, Igf1-CreER;Ai14
- GSM9514180 scRNA-seq of mouse microglia, MCAO Day 28, Zfp384 flox/flox control
- GSM9514181 scRNA-seq of mouse microglia, MCAO Day 28, Zfp384 cKO
- GSM9514182 scRNA-seq of mouse microglia, MCAO Day 28, ASO control
- GSM9514183 scRNA-seq of mouse microglia, MCAO Day 28, Zfp384 ASO
- GSM9514184 scRNA-seq of mouse brain cells, MCAO Day 28, ASO control
- GSM9514185 scRNA-seq of mouse brain cells, MCAO Day 28, Zfp384 ASO
- GSM9514186 scRNA-seq of mouse microglia, MCAO Day 56, ASO control
- GSM9514187 scRNA-seq of mouse microglia, MCAO Day 56, Zfp384 ASO
- GSM9514188 scRNA-seq of mouse brain cells, sham surgery, wild-type
- GSM9514189 scRNA-seq of mouse brain cells, MCAO Day 14, wild-type
- GSE343642 Single-cell RNA sequencing of peripheral blood and brain immune cells in mouse models of ischemic stroke 8 samples shares single-cell, ischemic, stroke, brain
- GSE225948 Brain and blood single-cell transcriptomic analysis in acute and subacute phases after experimental stroke 29 samples shares single-cell, stroke, brain
- GSE319237 Transcriptomic profiling of mouse microglia after ischemic stroke 15 samples shares microglia, ischemic, stroke
- GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares microglia, ischemic, stroke
- GSE300113 Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Main dataset) 59 samples shares microglia, 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
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares single-cell, brain
- GSE253581 Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB at 1-week, 1-month, and 3-months post-injection. 27 samples shares microglia, brain
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.