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Systems Biology-Based Assessment of Immune Responses to Whole Cell and Acellular Pertussis Vaccines: Rationale, Methodology and Enrollment Procedures for Omics Workflows

GSE281593 Homo sapiens (human) RNA-seq (gene expression) 79 samples Submitted 2025/08/20 Platform GPL17303
At a glance

RNA-seq (gene expression) · human · 79 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
79 samples: 39 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
Immunologic profiling of the infant immune response to whole-cell and acellular pertussis vaccinesNPJ vaccines · 2025
Summary (written by the submitters)
Given the local and systemic adverse reactions associated with whole cell pertussis vaccines combined with diphtheria and tetanus toxoids (DTP), acellular pertussis vaccines combined with the same toxoids (DTaP) were developed in the 1990s. In comparison to DTP, DTaP vaccines demonstrated reduced reactogenicity and equivalent or improved immunogenicity and efficacy.
Read the full summary ↓
However, there has been a resurgence of pertussis disease, particularly in DTaP-vaccinated children, suggesting that immunity wanes more quickly with DTaP vaccination. To elucidate the differences in immune responses to DTP and DTaP vaccines, we employed a systems biology-based strategy to compare global changes in gene expression following primary vaccination with either DTP or DTaP. We used RNA-Seq and ribosome profiling (RP) to identify transcriptional and translational signatures, respectively, in peripheral blood mononuclear cells (PBMCs) collected from 50 infant recipients of DTP or DTaP at two time-points (baseline (pre-vaccination at Day 1) and either Day 2 or 8 post-vaccination). We also used standard serologic methods to assess immunogenicity and correlated these results with the transcriptional and translational signatures. Here, we provide a detailed description of the rationale, experimental design, methodology and enrollment procedures used. Given the technical complexity of our approach, our objective is to fill knowledge gaps, describe key quality metrics, and support future publications. In brief, we recovered 4-12 million PBMCs (average 8.9 million) with 99% viability per 2.5 mL blood sample, enabling excellent nucleic acid recovery yields for preparation of high-quality sequencing libraries. In turn, these generated RNA-Seq and RP datasets with sufficient genome coverage, breadth, and depth to enable differential gene expression analyses, demonstrating the validity of our approach to study pertussis vaccine immunology specifically, and its utility to characterize mechanisms of the human immune response to vaccination generally.
Published in
Immunologic profiling of the infant immune response to whole-cell and acellular pertussis vaccines
Creech CB, Leguia M, Goll JB et al. · NPJ vaccines 2025 · PMID 40790123 · doi:10.1038/s41541-025-01170-5
This dataset
Open GSE281593 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 GSE281593_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 PRJNA1184764. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40790123) ↗
Study design
39 conditions, mostly in duplicate
SUB31, diphtheria and tetanus toxoids and who… ×2 SUB02, diphtheria and tetanus toxoids and ace… ×2 SUB06, diphtheria and tetanus toxoids and ace… ×2 SUB13, diphtheria and tetanus toxoids and ace… ×2 SUB17, diphtheria and tetanus toxoids and who… ×2 SUB16, diphtheria and tetanus toxoids and ace… ×2 SUB04, diphtheria and tetanus toxoids and ace… ×2 SUB08, diphtheria and tetanus toxoids and who… ×2 +32 more

Supports a between-group comparison across 78 samples.

How we read this: 39 replicated groups read from 79 sample titles; they account for 78 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

+ 39 more — browse all 79 samples with per-sample file links →

Datasets on a similar topic

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