Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [RNA]
Single-cell RNA-seq · mouse · 97 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
- 97 samples
- 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.
Read the full summary ↓
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 GSE98969_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 PRJNA387079 and SRA study SRP107339. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run AB1442 … AB2444 and carry no group information.
- GSM2629341 AB1442
- GSM2629342 AB1443
- GSM2629343 AB1444
- GSM2629344 AB1445
- GSM2629345 AB1446
- GSM2629346 AB1447
- GSM2629347 AB1448
- GSM2629348 AB1449
- GSM2629352 AB1547
- GSM2629353 AB1548
- GSM2629354 AB1549
- GSM2629355 AB1550
- GSM2629356 AB1551
- GSM2629357 AB1552
- GSM2629358 AB1553
- GSM2629359 AB1554
- GSM2629360 AB1555
- GSM2629361 AB1556
- GSM2629362 AB1557
- GSM2629363 AB1558
- GSM2629364 AB1667
- GSM2629365 AB1668
- GSM2629366 AB1709
- GSM2629367 AB1710
- GSM2629368 AB1711
- GSM2629369 AB1712
- GSM2629370 AB1713
- GSM2629371 AB1714
- GSM2629372 AB1715
- GSM2629373 AB1716
- GSM2629374 AB1717
- GSM2629375 AB1718
- GSM2629376 AB1719
- GSM2629377 AB1720
- GSM2629387 AB1730
- GSM2629388 AB1731
- GSM2629389 AB1732
- GSM2629390 AB1733
- GSM2629391 AB1734
- GSM2629392 AB1735
+ 57 more — browse all 97 samples with per-sample file links →
- GSE297298 Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer 18 samples shares identifies, rna-seq, type
- GSE327618 Targeting microglial phosphatidylethanolamine synthesis pathway promotes GABARAP-associated phagocytosis and A clearance in Alzheimer's disease 9 samples shares microglia, alzheimer
- GSE306116 Caspase-3 Control of RNA Splicing and Mitochondrial Dynamics in Microglia during Parkinson’s Disease [RNA-Seq] 12 samples shares microglia, rna-seq
- GSE306031 Single-Nucleus Transcriptomics Reveals Cell Type-Specific Remodeling and Epilepsy Associated Microglia 31 samples shares microglia, type
- GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares microglia, rna-seq
- 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
- GSE271535 Microglia innate immune memory is retained after enforced repopulation [RNA-seq] 29 samples shares microglia, rna-seq
- GSE285471 APOE genotype modifies the gene signature of microglial and astrocytic responses to aging 24 samples shares microglia, type
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.