Effect of stroke on the transcriptome of lamina propria macrophages in the small intestines
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 10 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 GSE216971_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 PRJNA896492 and SRA study SRP405609. 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 10 sample titles: 10 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.
- GSM6701499 Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 1)
- GSM6701500 Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 2)
- GSM6701501 Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 3)
- GSM6701502 Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 4)
- GSM6701503 Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 5)
- GSM6701504 Gut lamina propria macrophages sham vs pMCAO 24 h (pMCAO biol rep 1)
- GSM6701505 Gut lamina propria macrophages sham vs pMCAO 24 h (pMCAO biol rep 2)
- GSM6701506 Gut lamina propria macrophages sham vs pMCAO 24 h (pMCAO biol rep 3)
- GSM6701507 Gut lamina propria macrophages sham vs pMCAO 24 h (pMCAO biol rep 4)
- GSM6701508 Gut lamina propria macrophages sham vs pMCAO 24 h ( (pMCAO biol rep 5)
- GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares macrophages, stroke
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares macrophages
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares macrophages
- GSE309348 Whole transcriptome sequencing of UPEC-infected testis and epididymis (5d) following depletion of CX3CR1+ macrophages 18 samples shares macrophages
- GSE239287 Single-cell transcriptome sequencing of macrophages in acute kidney injury(AKI) to chronic kidney dieases(CKD) 17 samples shares macrophages
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages
- GSE265949 Effect of endothelial YAP/TAZ on neuroinflammation and outcome after ischemic stroke in mice 16 samples shares stroke
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares macrophages
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.