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Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop

GSE274944 Homo sapiens (human) RNA-seq (gene expression) 327 samples Submitted 2025/03/07 Platform GPL24676Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 327 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
327 samples: 57 conditions, mostly with about 5 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
Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loopNature communications · 2025
Summary (written by the submitters)
Outbreaks of Bordetella pertussis (BP), the causative agent of whooping cough, continue despite broad vaccination coverage and have been increasing since vaccination switched from whole-BP (wP) to acellular BP (aP) vaccines. wP vaccination has been associated with more durable protective immunity and an induced Th1 polarized memory T cell response.
Read the full summary ↓
Here, a multi-omics approach was applied to profile the immune response of 30 wP and 31 aP-primed individuals and identify correlates of T cell polarization before and after Tdap booster vaccination. We found that transcriptional changes indicating an interferon response on day 1 post-booster along with elevated plasma concentrations of IFN-γ and interferon-induced chemokines that peaked at day 1-3 post-booster correlated best with the Th1 polarization of the vaccine-induced memory T cell response on day 28. Our studies suggest that wP-primed individuals maintain their Th1 polarization through this early memory interferon response. This suggests that stimulating the interferon pathway during vaccination could be an effective strategy to elicit a predominant Th1 response in aP-primed individuals that protects better against infection.
Published in
Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop
Willemsen L, Lee J, Shinde P et al. · Nature communications 2025 · PMID 40169665 · doi:10.1038/s41467-025-58460-8
This dataset
Open GSE274944 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 GSE274944_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1148313 and SRA study SRP526486. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40169665) ↗
Study design
57 conditions, mostly with about 5 replicates each
1788_BP ×7 4654_BP ×7 4656_BP ×7 4657_BP ×7 6096_BP ×7 6097_BP ×7 6275_BP ×7 6279_BP ×7 +49 more

Supports a between-group comparison across 327 samples.

How we read this: 57 replicated groups read from 327 sample titles; they account for 327 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

+ 287 more — browse all 327 samples with per-sample file links →

Datasets on a similar topic

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