GEO series

scRNA-seq of Mycobacterium tuberculosis-specific CD4 T cells from Kenyan women with and wihtout HIV and before and after ART initiation following stimulation with Mtb WCL

GSE299662 Homo sapiens (human) Single-cell RNA-seq 14 samples Submitted 2025/07/10 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 14 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 14 samples: 14 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: Single-Cell Transcriptomics Reveals Depletion and Dysregulation of Mycobacterium tuberculosis-Specific Th1 and Th17 Cells Early After Acquisition of Human Immunodeficiency VirusThe Journal of infectious diseases · 2025

Summary (written by the submitters)

To understand how HIV and timing of ART initiation affect the transcriptional profile of Mtb-specific CD4 T cells, we performed 10X single-cell RNA sequencing comparing Mtb-specific CD4 T cell transcriptomes from people without HIV, people with HIV prior to ART, and people with HIV after ART from the Mombasa Cohort in Mombasa, Kenya. PBMCs were stimulated overnight with Mycobacterium tuberculosis whole cell lysate and CD40L+CD69+ Mtb-specifc CD4 T cells were sorted for sequencing.

Published in

Single-Cell Transcriptomics Reveals Depletion and Dysregulation of Mycobacterium tuberculosis-Specific Th1 and Th17 Cells Early After Acquisition of Human Immunodeficiency Virus

Pearson RA, Krish KN, Whatney WE et al. · The Journal of infectious diseases 2025 · PMID 40605619 · doi:10.1093/infdis/jiaf354

This dataset

Open GSE299662 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 GSE299662_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 PRJNA1275861 and SRA study SRP591647. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40605619) ↗

Study design

14 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 14 sample titles: 14 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

GSM9043146 Pool1_GEX
GSM9043147 Pool2_GEX
GSM9043148 Pool3_GEX
GSM9043149 Pool4_GEX
GSM9043150 Pool5_GEX
GSM9043151 Pool6_GEX
GSM9043152 Pool7_GEX
GSM9043153 Pool1_HTO
GSM9043154 Pool2_HTO
GSM9043155 Pool3_HTO
GSM9043156 Pool4_HTO
GSM9043157 Pool5_HTO
GSM9043158 Pool6_HTO
GSM9043159 Pool7_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.