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Effects on microglial morphology and function following CNS colonization by C. neoformans and its GXM capsule

GSE230212 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/03/12 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
12 samples: 12 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
Active Cryptococcus neoformans glucuronoxylomannan production prevents elimination of cryptococcal CNS infection in vivoJournal of neuroinflammation · 2025
Summary (written by the submitters)
Cryptococcus neoformans is an encapsulated basidiomycete fungus that has a predilection for the CNS, causing cryptococcal meningoencephalitis. This disease is most common in immunocompromised individuals such as patients with HIV+ or on immunosuppressive regimens. The fungus is inhaled from pigeon droppings and Eucalyptus tree bark. Once inhaled, the fungus travels from the airway into the bloodstream where it travels systemically into the CNS.
Read the full summary ↓
It has acquired three main ways of crossing the blood-brain barrier, but questions still exist about the dynamics of how the fungus colonizes the brain and how the host responds to this colonization. The fungus has three main virulence factors that allow it to colonize its hosts: antioxidant melanin production, immune-modulatory GXM polysaccharide capsule, and the ability to withstand physiological temperatures. Focusing on the effect of GXM, we saw that infection with the capsular H99 strain of C. neoformans, there was a decrease in mortality, while fungal burden and microglial migration to the cryptococcoma rose. There were also morphological changes in these microglial, so transcriptomics and functional migration and phagocytosis assays were conducted to evaluate the cellular activities at the site of infection. In summary, although microglia migrated and were recruited to the site of infection by the upregulation of pro-inflammatory pathways, they were unable to exert their functional roles due to a stonewall effect by GXM, as demonstrated by a reduction in migration to and phagocytosis of the fungus.
Published in
Active Cryptococcus neoformans glucuronoxylomannan production prevents elimination of cryptococcal CNS infection in vivo
Enriquez V, Munzen ME, Porras LM et al. · Journal of neuroinflammation 2025 · PMID 40038673 · doi:10.1186/s12974-025-03384-9
This dataset
Open GSE230212 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 GSE230212_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA957849 and SRA study SRP433642. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40038673) ↗
Study design
12 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 12 sample titles: 12 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
Datasets on a similar topic

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