GEO series
Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boosters
GSE297329
Homo sapiens (human)
Single-cell RNA-seq
98 samples
Submitted 2025/07/29
Platform GPL24676
At a glance
Single-cell RNA-seq · human · 98 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
- 98 samples: 95 distinct titles, 3 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.
- Paper
- Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boostersCell reports · 2025
Summary (written by the submitters)
We investigated the long-term impact of repeated COVID-19 vaccinations on adaptive immunity through a three-year study of 78 individuals without reported symptomatic infections. We observed distinct dynamics in Spike-specific responses across multiple vaccine doses. While antibody levels increased and stabilized with each booster, T cell responses quickly plateaued and remained stable.
Read the full summary ↓
Notably, approximately 30% of participants showed evidence of asymptomatic infections. Single-cell RNA sequencing revealed a diverse landscape of Spike-specific T cell phenotypes, without signs of exhaustion or functional impairment. Individuals with evidence of asymptomatic infection displayed unique immunological features, including increased frequencies of Th17-like CD4+ T cells and GZMKhi/IFNR CD8+ T cell subsets. In this group, repeated vaccinations correlated with an increase in regulatory T cells, potentially indicating a balanced immune response that may mitigate immunopathology. By regularly stimulating T cell memory, boosters contribute to a stable and enhanced immune response, which may provide better protection against symptomatic infections.
Published in
da Silva Antunes R, Fajardo-Rosas V, Yu ED et al.
· Cell reports 2025
· PMID 40580476
· doi:10.1016/j.celrep.2025.115907
This dataset
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.
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 GSE297329_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1263009 and SRA study SRP585333. Searching any of these in the dataset finder brings you back here.
Study design
95 distinct titles, 3 of them repeated
Pooled scRNA-seq library from multiple donors… ×2
Pooled scRNA-seq library from multiple donors… ×2
Pooled scRNA-seq library from multiple donors… ×2
How we read this: Read from 98 sample titles: 95 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
- GSM8988651 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST001_Hu_CD4_13D
- GSM8988652 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_1_CD4_12D
- GSM8988653 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_1_CD8_12D
- GSM8988654 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_2_CD4_12D
- GSM8988655 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_2_CD8_12D
- GSM8988656 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST003_Hu_1_CD4_13D
- GSM8988657 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST003_Hu_1_CD8_13D
- GSM8988658 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST003_Hu_2_CD4_13D
- GSM8988659 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST004_Hu_1_CD4_13D
- GSM8988660 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST004_Hu_2_CD4_13D
- GSM8988661 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST004_Hu_3_CD8_13D
- GSM8988662 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_1_CD4_13D
- GSM8988663 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_1_CD8_13D
- GSM8988664 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_2_CD4_13D
- GSM8988665 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_2_CD8_13D
- GSM8988666 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST006_Hu_CD4_13D
- GSM8988667 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST006_Hu_CD8_13D
- GSM8988668 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST007_Hu_CD4_13D
- GSM8988669 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_1_CD4_13D
- GSM8988670 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_1_CD8_13D
- GSM8988671 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_2_CD4_13D
- GSM8988672 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_2_CD8_13D
- GSM8988673 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD4_13D_1
- GSM8988674 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD4_13D_3
- GSM8988675 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD8_13D_2
- GSM8988676 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD8_13D_4
- GSM8988677 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_1_CD4
- GSM8988678 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_1_CD8
- GSM8988679 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_2_CD4
- GSM8988680 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_3_CD8
- GSM8988681 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_1_12
- GSM8988682 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_4_12
- GSM8988683 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_5_12
- GSM8988684 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_6_12
- GSM8988685 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_1_CD4_13D
- GSM8988686 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_1_CD8_13D
- GSM8988687 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_2_CD4_13D
- GSM8988688 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_2_CD8_13D
- GSM8988689 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_3_CD4_13D
- GSM8988690 Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_3_CD8_13D
+ 58 more — browse all 98 samples with per-sample file links →
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Share this dataset
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.