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Longitudinal analysis of antigen-specific T cells after Shingrix vaccination

GSE249632 Homo sapiens (human) Single-cell RNA-seq 2866 samples Submitted 2025/03/09 Platform GPL16791
At a glance

Single-cell RNA-seq · human · 2866 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
2866 samples: 6 conditions, mostly with about 96 replicates eachGroups 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
Longitudinal single cell profiling of epitope specific memory CD4+ T cell responses to recombinant zoster vaccineNature communications · 2025
Summary (written by the submitters)
SHINGRIX vaccination was used to investigate the fate of antigen specific memory CD4+ T cell at both cellular and transcriptional level upon immunization in a one-year longitudinal study. SHINGRIX is a subunit vaccine with glycoprotein E (gE) of varicella zoster virus (VZV) as the immunogen and requires two doses at least 60 days apart for protection against Herpes Zoster in adults over 50 years old.
Read the full summary ↓
Flow cytometry and single-cell RNA sequencing were used to evaluate cellular and transcriptomic changes of VZV gE epitope-specific CD4+ T cells in a TCR clonotypic fashion pre and post vaccination. Antigen-specific T cells remained at a higher frequency compared to baseline and retained markers of cell activation such as ICOS and PD1 even one year post-vaccination. Persistent TCR clonotypes amongst epitope-specific T-cells were common across different time points within each individual. Antigen-specific memory T cells with a dominant TCR clonotype at baseline remained at a relatively high frequency one year later after two doses of vaccine. In contrast, T cells with TCR clonotypes from naïve antigen specific cells at baseline could not be detected post-vaccination. Differential gene expression analyses of cells with identical TCR clonotypes show that cells post vaccination, including those at one year post vaccination, were distinct from cells at baseline, with upregulation of genes related to T cell differentiation, negative T cell regulation and T cell activation. Thus, in addition to an increase in frequency, committed memory T cells gain additional transcriptional changes upon vaccination that could alter the immune response against cognate immunogens compared to pre-vaccinated quiescent memory T cells.
Published in
Longitudinal single cell profiling of epitope specific memory CD4+ T cell responses to recombinant zoster vaccine
Wen X, Hu AK, Presnell SR et al. · Nature communications 2025 · PMID 40057520 · doi:10.1038/s41467-025-57562-7
This dataset
Open GSE249632 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 GSE249632_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 PRJNA1049847 and SRA study SRP476472. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40057520) ↗
Study design
6 conditions, mostly with about 96 replicates each
2_DR0701_Baseline_lib ×96 2_DR0701_Day 14_lib ×96 6_DR0404_Baseline_lib ×96 1_DR0401_Baseline_lib ×91 7_DR0401_Baseline_lib ×16 7_DR0101_Baseline_lib ×4 1_DR0701_Baseline_lib ×1

Supports a between-group comparison across 399 samples.

How we read this: 6 replicated groups read from the first 400 of 2866 sample titles; they account for 399 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

+ 2826 more — browse all 2866 samples with per-sample file links →

Datasets on a similar topic

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