GEO series
CD4+ T cells exhibit distinct transcriptional phenotypes in the lymph nodes and blood following mRNA vaccination in humans
GSE249313
Homo sapiens (human)
Single-cell RNA-seq
67 samples
Submitted 2024/05/31
Platform GPL24676
At a glance
Single-cell RNA-seq · human · 67 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
- 67 samples: 32 conditions, mostly in duplicateGroups 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
- CD4(+) T cells exhibit distinct transcriptional phenotypes in the lymph nodes and blood following mRNA vaccination in humansNature immunology · 2024
Summary (written by the submitters)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mRNA vaccination induce robust CD4+ T cell responses. Using single-cell transcriptomics, here, we evaluated CD4+ T cells specific for the SARS-CoV-2 spike protein in the blood and draining lymph nodes (dLNs) of individuals 3 months and 6 months after vaccination with the BNT162b2 mRNA vaccine.
Read the full summary ↓
We analyzed 1,277 spike-specific CD4+ T cells, including 238 defined using Trex, a deep learning-based reverse epitope mapping method to predict antigen specificity. Human dLN spike-specific CD4+ follicular helper T (TFH) cells exhibited heterogeneous phenotypes, including germinal center CD4+ TFH cells and CD4+IL-10+ TFH cells. Analysis of an independent cohort of SARS-CoV-2-infected individuals 3 months and 6 months after infection found spike-specific CD4+ T cell profiles in blood that were distinct from those detected in blood 3 months and 6 months after BNT162b2 vaccination. Our findings provide an atlas of human spike-specific CD4+ T cell transcriptional phenotypes in the dLNs and blood following SARS-CoV-2 vaccination or infection.
Published in
Borcherding N, Kim W, Quinn M et al.
· Nature immunology 2024
· PMID 39164479
· doi:10.1038/s41590-024-01888-9
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 GSE249313_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 PRJNA1047676 and SRA study SRP475399. Searching any of these in the dataset finder brings you back here.
Study design
32 conditions, mostly in duplicate
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
scRNA-seq and TCR profiling of Homo Spaiens: … ×2
+27 more
Supports a between-group comparison across 64 samples.
How we read this: 32 replicated groups read from 67 sample titles; they account for 64 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
- GSM7933456 scRNA-seq and TCR profiling of Homo Spaiens: 350-041 d14 peripheral blood bio rep 1
- GSM7933457 scRNA-seq and TCR profiling of Homo Spaiens: 350-041 d14_peripheral blood bio rep 2
- GSM7933458 scRNA-seq and TCR profiling of Homo Spaiens: 350-041 m6 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933459 scRNA-seq and TCR profiling of Homo Spaiens: 350-041 m6 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933460 scRNA-seq and TCR profiling of Homo Spaiens: 350-065 d28 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933461 scRNA-seq and TCR profiling of Homo Spaiens: 350-065 d28 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933462 scRNA-seq and TCR profiling of Homo Spaiens: 350-084 d28 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933463 scRNA-seq and TCR profiling of Homo Spaiens: 350-084 d28 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933464 scRNA-seq and TCR profiling of Homo Spaiens: 350-117 d28 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933465 scRNA-seq and TCR profiling of Homo Spaiens: 350-117 d28 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933466 scRNA-seq and TCR profiling of Homo Spaiens: 350-117 m6 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933467 scRNA-seq and TCR profiling of Homo Spaiens: 350-117 m6 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933468 scRNA-seq and TCR profiling of Homo Spaiens: 350-397 d14 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933469 scRNA-seq and TCR profiling of Homo Spaiens: 350-397 d14 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933470 scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d28 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933471 scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d28 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933472 scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d84 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933473 scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d84 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933474 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 lymph node bio rep 1 scRNA-seq and TCR profi…
- GSM7933475 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 lymph node bio rep 2 scRNA-seq and TCR profi…
- GSM7933476 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933477 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933478 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 lymph node bio rep 1 scRNA-seq and TCR profi…
- GSM7933479 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 lymph node bio rep 2 scRNA-seq and TCR profi…
- GSM7933480 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933481 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933482 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d28 lymph node bio rep 1 scRNA-seq and TCR profi…
- GSM7933483 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d28 lymph node bio rep 2 scRNA-seq and TCR profi…
- GSM7933484 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d60 lymph node bio rep 1 scRNA-seq and TCR profi…
- GSM7933485 scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d60 lymph node bio rep 2 scRNA-seq and TCR profi…
- GSM7933486 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d110 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933487 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d110 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933488 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d201 peripheral blood bio rep 1 scRNA-seq and TCR profi…
- GSM7933489 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d201 peripheral blood bio rep 2 scRNA-seq and TCR profi…
- GSM7933490 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d28 lymph node bio rep 1 scRNA-seq and TCR profi…
- GSM7933491 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d28 lymph node bio rep 2 scRNA-seq and TCR profi…
- GSM7933492 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d60 lymph node bio rep 1 scRNA-seq and TCR profi…
- GSM7933493 scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d60 lymph node bio rep 2 scRNA-seq and TCR profi…
- GSM7933494 scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d110 lymph node bio rep 1
- GSM7933495 scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d110 peripheral blood bio rep 1 scRNA-seq and TCR profi…
+ 27 more — browse all 67 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.