GEO series

ACCELERATED CD8+ T CELL MATURATION IN INFANTS WITH PERINATAL HIV INFECTION

GSE254645 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2024/04/16 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 28 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: 28 samples: 28 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: A role for Fas/FasL-dependent NK-mediated cytotoxicity in infants with perinatal HIViScience · 2025

Summary (written by the submitters)

In perinatal HIV infection, early ART initiation is recommended but questions remain regarding infant immune responses to HIV and impact of HIV on immune development. Using single cell transcriptional and phenotypic analysis we evaluated the T cell compartment at pre-ART initiation of infants with perinatally acquired HIV from Maputo, Mozambique (TARA cohort).

Read the full summary ↓

CD8+ T cell maturation subsets exhibited altered distribution in HIV exposed infected (HEI) infants relative to control infants (HIV exposed uninfected) with reduced naïve, increased effectors, higher frequencies of activated T cells, and lower frequencies of cells with markers of self-renewal. Additionally, a cluster of CD8+ T cells identified in HEI displayed gene profiles consistent with cytotoxic T lymphocytes (CTL) and showed evidence for hyper expansion. Longitudinal phenotypic analysis revealed accelerated maturation of CD8+ T cells was maintained in HEI despite viral control. The results point to a HIV directed immune response that is likely to influence reservoir establishment.

Published in

A role for Fas/FasL-dependent NK-mediated cytotoxicity in infants with perinatal HIV

Iyer A, de Armas L, Dinh V et al. · iScience 2025 · PMID 41210967 · doi:10.1016/j.isci.2025.113637

This dataset

Open GSE254645 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 GSE254645_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 PRJNA1071184 and SRA study SRP486932. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41210967) ↗

Study design

28 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 28 sample titles: 28 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

GSM8047693 PBMC, HIV Exposed Uninfected (HEU), CE21M, Gene Expression (GEX)
GSM8047694 PBMC, HIV Exposed Uninfected (HEU), CE21M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047695 PBMC, HIV Exposed Uninfected (HEU), CE21M, TCR
GSM8047696 PBMC, HIV Exposed Uninfected (HEU), CE21M, BCR
GSM8047697 PBMC, HIV Exposed Uninfected (HEU), CE25M, Gene Expression (GEX)
GSM8047698 PBMC, HIV Exposed Uninfected (HEU), CE25M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047699 PBMC, HIV Exposed Uninfected (HEU), CE25M, TCR
GSM8047700 PBMC, HIV Exposed Uninfected (HEU), CE25M, BCR
GSM8047701 PBMC, HIV Exposed Uninfected (HEU), CE37M, Gene Expression (GEX)
GSM8047702 PBMC, HIV Exposed Uninfected (HEU), CE37M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047703 PBMC, HIV Exposed Uninfected (HEU), CE37M, TCR
GSM8047704 PBMC, HIV Exposed Uninfected (HEU), CE37M, BCR
GSM8047705 PBMC, HIV Exposed Infected (HEI), CP2M, Gene Expression (GEX)
GSM8047706 PBMC, HIV Exposed Infected (HEI), CP2M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047707 PBMC, HIV Exposed Infected (HEI), CP2M, TCR
GSM8047708 PBMC, HIV Exposed Infected (HEI), CP2M, BCR
GSM8047709 PBMC, HIV Exposed Infected (HEI), CP3M, Gene Expression (GEX)
GSM8047710 PBMC, HIV Exposed Infected (HEI), CP3M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047711 PBMC, HIV Exposed Infected (HEI), CP3M, TCR
GSM8047712 PBMC, HIV Exposed Infected (HEI), CP3M, BCR
GSM8047713 PBMC, HIV Exposed Infected (HEI), CP6M, Gene Expression (GEX)
GSM8047714 PBMC, HIV Exposed Infected (HEI), CP6M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047715 PBMC, HIV Exposed Infected (HEI), CP6M, TCR
GSM8047716 PBMC, HIV Exposed Infected (HEI), CP6M, BCR
GSM8047717 PBMC, HIV Exposed Infected (HEI), CP18M, Gene Expression (GEX)
GSM8047718 PBMC, HIV Exposed Infected (HEI), CP18M, Feature Barcode/Antibody Derived Tag (FB/ADT)
GSM8047719 PBMC, HIV Exposed Infected (HEI), CP18M, TCR
GSM8047720 PBMC, HIV Exposed Infected (HEI), CP18M, BCR

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GSE332711 CD4/CD8 ratio is associated with structural reorganization of vaccine-induced immune responses in people living with HIV 60 samples shares cd8, hiv
GSE210231 CD8+ T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance 931 samples shares cd8
GSE272993 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 1] 360 samples shares cd8
GSE225063 Blockade of LAG-3 and PD-1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8+ T cells to promote antitumor immunity 256 samples shares cd8
GSE288199 Distinct CD8+ T cell dynamics associate with response to neoadjuvant cancer immunotherapies 180 samples shares cd8

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