Single cell gene expression from the hippocampus of 5xFAD mice subjected to stroke
Single-cell RNA-seq · mouse · 10 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
- 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 GSE266033_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 PRJNA1105371 and SRA study SRP504411. 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.
- GSM8239678 25.4 WT Sham
- GSM8239679 25.4 WT MCAO
- GSM8239680 28.8 WT Sham
- GSM8239681 28.8 WT MCAO
- GSM8239682 28.2 WT Sham
- GSM8239683 28.2 WT MCAO
- GSM8239684 28.5 5xFAD Sham
- GSM8239685 28.5 5xFAD MCAO
- GSM8239686 29.4 5xFAD Sham
- GSM8239687 29.4 5xFAD MCAO
- GSE302153 Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer’s Disease 32 samples shares 5xfad, hippocampus
- GSE276797 Gene expression profile at single cell level of immune cells from the deep cervical lymph nodes (dCLNs), superficial cervical lymph nodes (sCLNs), and inguinal lymph nodes (iLNs) of wild-type (WT) and Alzheimer's disease (AD) transgenic animals (5xFAD) 34 samples shares 5xfad
- GSE296886 Effect of a natural product derivative on gene expression signatures in 5xFAD transgenic mice 25 samples shares 5xfad
- GSE262881 A single-cell transcriptomic atlas of all cell types in the entire 5xFAD mouse brain in response to dietary inulin supplementation 24 samples shares 5xfad
- GSE215439 Effect of metronidazole on microglial gene expression and gut microbiome composition in the 5XFAD mice model of Alzheimer's disease 20 samples shares 5xfad
- GSE319850 Astrocytic APOE3-Christchurch expression ameliorates brain amyloid-β pathology in 5xFAD mice 23 samples shares 5xfad
- GSE255004 Sensory Flicker Stimulation of 5xFAD Mice Activates Immune Pathways in a Frequency and Time Dependent Manner 176 samples shares 5xfad
- GSE295077 Cell-type-specific contributions to impaired blood-brain barrier and altered cerebral metabolism in prodromal 5XFAD mice 16 samples shares 5xfad
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.