GEO series

Diverse subpopulations of reactive mouse astrocytes following chronic Toxoplasma infection.

GSE274474 Mus musculus (mouse) Single-cell RNA-seq 11 samples Submitted 2024/08/30 Platform GPL24247Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 11 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: 11 samples: 11 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.

Summary (written by the submitters)

Astrocytes provide physical and metabolic support for neurons, regulate the blood brain barrier, and react to injury, infection, and disease. When astrocytes become reactive, the regulation of the inflammatory state, the forms it takes, and its longevity are all poorly understood. Several models of acute inflammation have revealed astrocyte subpopulations that go beyond a two-activation state model, instead encompassing distinct functional subsets.

Read the full summary ↓

However, how reactive astrocyte (RA) subsets evolve over time during chronic inflammatory disease or infection have been technically difficult to address. Here we use a prolific human pathogen, Toxoplasma gondii, that causes lifelong infection in the brain alongside a novel Lcn2CreERT2 reporter mouse line to examine astrocyte subsets during chronic inflammation. Single cell RNA sequencing revealed diverse astrocyte populations during chronic inflammation. Furthermore, we observed transcriptionally unique Lcn2CreERT2+ RAs, some of which changed over time in a manner suggestive of potential resolution and overall plasticity of RAs. In addition to an immune regulating Lcn2CreERT2+ astrocyte population enriched with gene transcripts encoding chemokines Ccl5, Cxcl9, Cxcl10 and receptors Ccr7 and Il7r, a specific set of Lcn2CreERT2+ astrocytes highly expressed transthyretin (Ttr), a secreted carrier protein involved in glycolytic enzyme activation and potential vasculature regulation and angiogenesis. These findings provide novel information about the evolution and diversity of reactive astrocyte subtypes and functional signatures at different stages of infection and an undocumented role for transthyretin expressing astrocytes in immune regulation at the central nervous system (CNS) vasculature.

This dataset

Open GSE274474 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 GSE274474_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 PRJNA1146474 and SRA study SRP525456. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

11 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 11 sample titles: 11 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

GSM8449838 Lcn2CreErt2;Ai9, 14dpi, scRNAseq
GSM8449839 Lcn2CreErt2;Ai9, 42dpi, scRNAseq
GSM8449840 Lcn2CreErt2;Ai9, Tamoxifen Rested, scRNAseq
GSM8449841 Sorted ACSA2 Astrocytes, 14dpi, scRNAseq
GSM8449842 Sorted ACSA2 Astrocytes, 28dpi, scRNAseq
GSM8449843 Sorted ACSA2 Astrocytes, 42dpi, scRNAseq
GSM8449844 Sorted ACSA2 Astrocytes, Naive, scRNAseq
GSM8449845 14dpi, scRNAseq
GSM8449846 28dpi, scRNAseq
GSM8449847 42dpi, scRNAseq
GSM8449848 Naive, scRNAseq

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Search all mouse RNA-seq datasets in GEO →

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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.