Transcriptomic profiling of mouse microglia after ischemic stroke
RNA-seq (gene expression) · mouse · 15 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 15 samples: 11 distinct titles, 2 of them repeatedGroups 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 GSE319237_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1422659 and SRA study SRP676487. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 15 sample titles: 11 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.
- GSM9514163 RNA-seq of mouse microglia, sham surgery, wild-type
- GSM9514164 RNA-seq of mouse microglia, MCAO day 1, wild-type
- GSM9514165 RNA-seq of mouse microglia, MCAO day 6, wild-type
- GSM9514166 RNA-seq of mouse microglia, MCAO day 14, wild-type
- GSM9514167 RNA-seq of mouse microglia, MCAO day 28, wild-type
- GSM9514168 RNA-seq of mouse microglia, MCAO day 6, Igf1-Egfp EGFP–
- GSM9514169 RNA-seq of mouse microglia, MCAO day 6, Igf1-Egfp EGFP+
- GSM9514170 RNA-seq of mouse microglia, MCAO day 14, Igf1-Egfp EGFP–
- GSM9514171 RNA-seq of mouse microglia, MCAO day 14, Igf1-Egfp EGFP+
- GSM9514172 RNA-seq of mouse microglia, MCAO day 6, Yy1flox/flox control replicate 1
- GSM9514173 RNA-seq of mouse microglia, MCAO day 6, Yy1flox/flox control replicate 2
- GSM9514174 RNA-seq of mouse microglia, MCAO day 6, Yy1flox/flox control replicate 3
- GSM9514175 RNA-seq of mouse microglia, MCAO day 6, Cx3cr1-CreER;Yy1flox/flox replicate 1
- GSM9514176 RNA-seq of mouse microglia, MCAO day 6, Cx3cr1-CreER;Yy1flox/flox replicate 2
- GSM9514177 RNA-seq of mouse microglia, MCAO day 6, Cx3cr1-CreER;Yy1flox/flox replicate 3
- GSE319238 Single-cell transcriptomic analysis of microglia and brain cells after ischemic stroke 12 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
- GSE220043 Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke 22 samples shares microglia, ischemic, stroke
- GSE265949 Effect of endothelial YAP/TAZ on neuroinflammation and outcome after ischemic stroke in mice 16 samples shares ischemic, stroke
- GSE280862 Loss of Sarm1 Mitigates Axonal Degeneration and Promotes Neuronal Regeneration After Ischemic Stroke 15 samples shares ischemic, stroke
- GSE343642 Single-cell RNA sequencing of peripheral blood and brain immune cells in mouse models of ischemic stroke 8 samples shares ischemic, stroke
- GSE276260 H2O2-induced astrocytic collagen triggers neuronal death in ischemic stroke [RNA-seq] 9 samples shares ischemic, stroke
- GSE304010 A transcriptomic microglia taxonomy across mouse and human pathologies 74 samples shares microglia
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.