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HIV infection exacerbates ischemic brain injury through dysregulating phagocytosis and neuroinflammatory signals in macrophages/microglia via C1ql2

GSE335736 Mus musculus (mouse) RNA-seq (gene expression) 8 samples Submitted 2026/06/30 Platform GPL23479
At a glance

RNA-seq (gene expression) · mouse · 8 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
8 samples: 2 × Sham operation vs 2 × MCAO vs 2 × HIV&MCAO vs 2 × Antiviral drug&HIV&MCAOGroups 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)
The incidence of human immunodeficiency virus (HIV)-infected individuals is greater, and outcomes are worse following cerebral stroke, despite widespread access to antiretroviral therapy. As the major reservoir of HIV, resident microglia and infiltrative macrophages in the brain can be aberrantly activated by HIV after stroke. However, the underlying reason driving these pathological processes in poststroke brain injury remains unclear.
Read the full summary ↓
Herein, with the use of ischemia mice and oxygen-glucose deprivation models, we revealed that HIV infection induced a proinflammatory phenotype and impaired the phagocytic clearance of dead/dying neurons by macrophages/microglia, which was accompanied by a marked reduction in complement C1q-like protein (C1ql) 2 in both peri-infarct macrophages/microglia and cerebrospinal fluid. Importantly, these pathological changes, with ischemia-induced neural demyelination, were strongly mitigated by the intracerebral delivery of recombinant C1ql2, which culminated in a reduced infarct volume and neurological deficits poststroke. Notably, delivering recombinant C1ql2 in the presence of gavage antiretroviral drug Biktarvy further promoted functional recovery and rescued tissue loss following chronic ischemia in HIV-bearing mice, underscoring its potential therapeutic relevance. Collectively, these findings reveal a previously unrecognized C1ql2-dependent mechanism through which HIV infection impairs poststroke repair, which highlights C1ql2 restoration as a promising neuroprotective strategy for HIV-infected stroke patients.
This dataset
Open GSE335736 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 GSE335736_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 PRJNA1479353 and SRA study SRP710359. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
2 × Sham operation vs 2 × MCAO vs 2 × HIV&MCAO vs 2 × Antiviral drug&HIV&MCAO

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 of them. 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
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