GEO series

Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB at 1-week, 1-month, and 3-months post-injection.

GSE253581 Mus musculus (mouse) Single-cell RNA-seq 27 samples Submitted 2024/05/29 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 27 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 27 samples: 27 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.
Paper: S100A8-enriched microglia populate the brain of tau-seeded and accelerated aging miceAging cell · 2024

Summary (written by the submitters)

To gain deeper insights into the relationship between Tau spreading and microglial response, we conducted a comprehensive analysis of microglial heterogeneity in K18-seeded P301L mice at 1 week, 1 month, and 3 months post-injection. We compared these findings with those from control groups: P301L mice injected with PBS and their non-transgenic counterparts, the FVB mice also subjected to PBS injection. For this purpose, we employed CITE-seq to investigate CD11b positive cells isolated from cerebellum and olfactory bulb-removed brains.

Published in

S100A8-enriched microglia populate the brain of tau-seeded and accelerated aging mice

Gruel R, Bijnens B, Van Den Daele J et al. · Aging cell 2024 · PMID 38403918 · doi:10.1111/acel.14120

This dataset

Open GSE253581 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE253581_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1066313 and SRA study SRP484544. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38403918) ↗

Study design

27 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 27 sample titles: 27 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.

Samples in this study

GSM8023809 1-week PI PBS-injected FVB, GEX
GSM8023810 1-week PI PBS-injected FVB, ADT
GSM8023811 1-week PI PBS-injected FVB,HTO
GSM8023812 1-week PI PBS-injected P301L, GEX
GSM8023813 1-week PI PBS-injected P301L, ADT
GSM8023814 1-week PI PBS-injected P301L,HTO
GSM8023815 1-week PI K18-seeded P301L, GEX
GSM8023816 1-week PI K18-seeded P301L, ADT
GSM8023817 1-week PI K18-seeded P301L,HTO
GSM8023818 1-month PI PBS-injected FVB, GEX
GSM8023819 1-month PI PBS-injected FVB, ADT
GSM8023820 1-month PI PBS-injected FVB,HTO
GSM8023821 1-month PI PBS-injected P301L, GEX
GSM8023822 1-month PI PBS-injected P301L, ADT
GSM8023823 1-month PI PBS-injected P301L,HTO
GSM8023824 1-month PI K18-seeded P301L, GEX
GSM8023825 1-month PI K18-seeded P301L, ADT
GSM8023826 1-month PI K18-seeded P301L,HTO
GSM8023827 3-months PI PBS-injected FVB, GEX
GSM8023828 3-months PI PBS-injected FVB, ADT
GSM8023829 3-months PI PBS-injected FVB,HTO
GSM8023830 3-months PI PBS-injected P301L, GEX
GSM8023831 3-months PI PBS-injected P301L, ADT
GSM8023832 3-months PI PBS-injected P301L,HTO
GSM8023833 3-months PI K18-seeded P301L, GEX
GSM8023834 3-months PI K18-seeded P301L, ADT
GSM8023835 3-months PI K18-seeded P301L,HTO

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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.