The effect of cGAS or STING knockout on gene expression changes in mouse brain after ischemic stroke
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 6 conditions, mostly in duplicateGroups 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
- Blocking cGAS-STING pathway promotes post-stroke functional recovery in an extended treatment window via facilitating remyelinationMed (New York, N.Y.) · 2024
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 GSE226410_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 PRJNA940144 and SRA study SRP425219. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 of them. 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.
- GSM7074642 14d_cGAS-KO_1 14d_cGAS-KO
- GSM7074643 14d_cGAS-KO_2 14d_cGAS-KO
- GSM7074644 14d_STING-KO_1 14d_STING-KO
- GSM7074645 14d_STING-KO_2 14d_STING-KO
- GSM7074646 14d_WT_1 14d_WT
- GSM7074647 14d_WT_2 14d_WT
- GSM7074648 7d_cGAS-KO_1 7d_cGAS-KO
- GSM7074649 7d_cGAS-KO_2 7d_cGAS-KO
- GSM7074650 7d_STING-KO_1 7d_STING-KO
- GSM7074651 7d_STING-KO_2 7d_STING-KO
- GSM7074652 7d_WT_1 7d_WT
- GSM7074653 7d_WT_2 7d_WT
- GSE220043 Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke 22 samples shares sting, ischemic, stroke
- GSE319238 Single-cell transcriptomic analysis of microglia and brain cells after ischemic stroke 12 samples shares ischemic, stroke, brain
- GSE343642 Single-cell RNA sequencing of peripheral blood and brain immune cells in mouse models of ischemic stroke 8 samples shares ischemic, stroke, brain
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares sting, brain
- GSE241587 Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin cardiomyopathy mice [sci-RNA-seq] 96 samples shares sting, cgas
- GSE241725 Evolutionarily conserved role of Telomerase reverse transcriptase (TERT) in programming the microenvironment via regulation of cGAS/STING pathway 15 samples shares sting, cgas
- GSE315829 Investigate changes in gene expression and enriched pathways in endothelial cells following Liver endothelial Heg1 knockout. 13 samples shares knockout, changes
- GSE233837 Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain 24 samples shares changes, 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.