Plaque-induced transcriptional reprogramming of microglia towards lymphoid receptor expression protects against Alzheimer's disease [scRNA-seq]
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: 10 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.
- Paper
- Lymphoid gene expression supports neuroprotective microglia functionNature · 2025
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 GSE296768_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 PRJNA1261025 and SRA study SRP584211. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 12 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.
- GSM8976271 8 month control, replicate 1
- GSM8976272 8 month 5xFAD, replicate 1
- GSM8976273 8 month control, replicate 2
- GSM8976274 8 month 5xFAD, replicate 2
- GSM8976275 3 month 5xFAD
- GSM8976276 3 month 5xFAD; Cd28-cKO
- GSM8976277 6 month control, replicate 1
- GSM8976278 6 month 5xFAD, replicate 1
- GSM8976279 6 month 5xFAD; Cd28-cKO, replicate 1
- GSM9011862 3 month control
- GSM9011863 3 month 5xFAD, replicate 1
- GSM9011864 3 month 5xfAD; Cd28-cKO, replicate 1
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares microglia, scrna-seq
- GSE98969 Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [RNA] 97 samples shares microglia, alzheimer
- 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, alzheimer
- GSE223424 Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease 57 samples shares microglia, alzheimer
- GSE278199 Microglia regulate cortical remyelination via ΤNFR1-dependent phenotypic polarization [scRNA-Seq] 45 samples shares microglia, scrna-seq
- GSE307127 Immune Receptor Lag3 Deletion Alleviates Neurodegeneration Phenotypes in a Mouse Model of Alzheimer’s Disease 36 samples shares alzheimer, receptor
- GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares microglia, scrna-seq
- GSE327604 Epigenetic control of microglial mitochondrial immunity by KAT7 drives Alzheimer’s disease pathogenesis [RNA-Seq] 12 samples shares microglia, alzheimer
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.