GEO series

CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [scTCR-seq, CITE-seq]]

GSE210229 Homo sapiens (human) Single-cell RNA-seq 14 samples Submitted 2024/04/01 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: CD8(+) T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominanceCell reports · 2024

Summary (written by the submitters)

mRNA vaccines against the Spike glycoprotein of severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, it is unknown whether the repertoire of memory T cell clones changes between primary and secondary vaccinations. Here, we analyzed the kinetic profile of Spike-reactive T-cell clones before the first dose, one week after the first and second dose, and four weeks after the second dose of the BNT162b mRNA vaccine.

Read the full summary ↓

Interestingly, a new set of Spike-reactive CD8+ T cell clones exhibited the greatest expansion following secondary vaccination and replaced the clones that had responded to the primary vaccination. Single-cell mRNA/protein/TCR analysis revealed that the first-responder clones exhibited a terminally differentiated phenotype, whereas second-responder clones exhibited an actively proliferating phenotype. These results show that Spike-reactive T cell responses induced by repetitive mRNA vaccination are augmented and maintained by replacement with newly-generated clones with proliferative potential.

Published in

CD8(+) T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance

Aoki H, Kitabatake M, Abe H et al. · Cell reports 2024 · PMID 38458195 · doi:10.1016/j.celrep.2024.113887

This dataset

Open GSE210229 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 GSE210229_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 PRJNA864804 and SRA study SRP389140. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38458195) ↗

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

GSM6424219 ID2_Abseq_P3
GSM6424220 ID2_Target_P3
GSM6424221 ID2_TCR_P3
GSM6424222 ID27_Abseq_P3
GSM6424223 ID27_Target_P3
GSM6424224 ID27_TCR_P3
GSM7329944 Batch2-1_Abseq
GSM7329945 Batch2-1_Target
GSM7329946 Batch2-1_TCR
GSM7329947 Batch2-1_Tag
GSM7329948 Batch2-2_Abseq
GSM7329949 Batch2-2_Target
GSM7329950 Batch2-2_TCR
GSM7329951 Batch2-2_Tag

Datasets on a similar topic

GSE210231 CD8+ T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance 931 samples shares sars-cov-2, cd8, characterized, vaccinations, successive
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GSE308745 The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[PB cohort2] 87 samples shares cd8
GSE260763 Expansion of memory Vδ2 T cells following SARS-CoV-2 vaccination revealed by temporal single-cell transcriptomics 60 samples shares sars-cov-2
GSE298811 Immune dysregulation and stem-like CD8+ T cell enrichment in type 1 diabetes pancreatic lymph nodes 57 samples shares cd8

Search all human RNA-seq datasets in GEO →

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