GEO series

Contribution of cytotoxic CD8 T cells, neutrophils and type 1 interferon signaling to hyperinflammatory pathology in HIV associated TB meningitis

GSE324044 Homo sapiens (human) Single-cell RNA-seq 64 samples Submitted 2026/03/10 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 64 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: Homo sapiens (human)
Samples: 64 samples: 53 distinct titles, 11 of them repeatedGroups 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)

Immune dysregulation contributes to death and disability in tuberculous meningitis. People living with HIV have the highest risk of TBM, greatest death and disability, and the least evidence that anti-inflammatory therapy improves the poor outcome. Improving therapy relies on a more refined understanding of the host immune response. Using single-cell RNA sequencing, we characterised 188,983 lumbar CSF cells from 25 adults with HIV-associated TBM and identified correlates of bacterial load.

Read the full summary ↓

There was heterogeneity in cell composition between patients, but cytotoxic CD8 T cells with low cytokine expression were consistently predominant with a large number expressing GZMK, known to activate complement. In microbiologically-confirmed TBM, there was greater cytotoxicity in T, NK and γδ cells, and higher type 1 interferon stimulation in T and B lymphocytes. Neutrophils expressed markers suggesting heightened cytokine stimulation, enhanced effector function, and IL-8-mediated peripheral neutrophil recruitment. In a separate longitudinal cohort, type 1 interferon signalling increased in the blood and CSF following treatment initiation. Overall, findings indicate a hyper-inflammatory immune response in the CSF of HIV-associated TBM patients characterised by an accumulation of granzyme-rich cytotoxic CD8 T cells, highly activated neutrophils and host-detrimental type 1 IFN signalling.

This dataset

Open GSE324044 in finder → Find more human 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 GSE324044_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 PRJNA1433277 and SRA study SRP681624. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

53 distinct titles, 11 of them repeated

Patient 6, TBM, CSF, D ×2 Patient 8, TBM, CSF, D ×2 Patient 10, TBM, CSF, D ×2 Patient 12, TBM, CSF, D ×2 Patient 19, TBM, CSF, D ×2 Patient 40, TBM, CSF, D ×2 Patient 43, TBM, CSF, D ×2 Patient 50, TBM, CSF, D ×2 +3 more

How we read this: Read from 64 sample titles: 53 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

GSM9567297 Patient 5, TBM, CSF, D28
GSM9567298 Patient 6, TBM, CSF, D3
GSM9567299 Patient 6, TBM, CSF, D28
GSM9567300 Patient 7, TBM, CSF, D3
GSM9567301 Patient 8, TBM, CSF, D3
GSM9567302 Patient 8, TBM, CSF, D28
GSM9567303 Patient 9, TBM, CSF, D3
GSM9567304 Patient 10, TBM, CSF, D3
GSM9567305 Patient 10, TBM, CSF, D28
GSM9567306 Patient 11, TBM, CSF, D28
GSM9567307 Patient 12, TBM, CSF, D3
GSM9567308 Patient 12, TBM, CSF, D28
GSM9567309 Patient 13, TBM, CSF, D3
GSM9567310 Patient 14, TBM, CSF, D3
GSM9567311 Patient 15, TBM, CSF, D3
GSM9567312 Patient 16, TBM, CSF, D3
GSM9567313 Patient 17, TBM, CSF, D3
GSM9567314 Patient 18, TBM, CSF, D3
GSM9567315 Patient 19, TBM, CSF, D3
GSM9567316 Patient 19, TBM, CSF, D28
GSM9567317 Patient 20, TBM, CSF, D28
GSM9567318 Patient 21, TBM, CSF, D3
GSM9567319 Patient 39, TBM, CSF, D28
GSM9567320 Patient 40, TBM, CSF, D7
GSM9567321 Patient 40, TBM, CSF, D28
GSM9567322 Patient 41, TBM, CSF, D7
GSM9567323 Patient 42, TBM, CSF, D7
GSM9567324 Patient 43, TBM, CSF, D7
GSM9567325 Patient 43, TBM, CSF, D28
GSM9567326 Patient 44, TBM, CSF, D7
GSM9567327 Patient 45, TBM, CSF, D7
GSM9567328 Patient 46, TBM, CSF, D7
GSM9567329 Patient 47, TBM, CSF, D7
GSM9567330 Patient 48, TBM, CSF, D7
GSM9567331 Patient 49, TBM, CSF, D28
GSM9567332 Patient 50, TBM, CSF, D7
GSM9567333 Patient 50, TBM, CSF, D28
GSM9567334 Patient 51, TBM, CSF, D7
GSM9567335 Patient 1, TBM, CSF, D3
GSM9567336 Patient 52, TBM, CSF, D7

+ 24 more — browse all 64 samples with per-sample file links →

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GSE332837 Single-cell sequencing reveals NK cell dysregulation during chronic HIV infection and identifies transitional NK cell cytotoxicity related to HIV reservoir decay 39 samples shares hiv, cytotoxic
GSE291537 Epigenetically controlled ZEB2 expression promotes the cytotoxic potential of CMV-specific CD8+ T cells 12 samples shares cd8, cytotoxic
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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.