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Obese individuals exhibit distinct temporal gene expression dynamics in response to influenza vaccination

GSE271520 Homo sapiens (human) RNA-seq (gene expression) 489 samples Submitted 2025/06/25 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 489 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
489 samples: 163 × blood, Day 3, UGA4, vs 163 × blood, Day 7, UGA4, vs 74 × blood, Day 28, UGA4,Groups 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
Obese individuals exhibit distinct temporal gene expression dynamics in response to influenza vaccinationMicrobiology spectrum · 2025
Summary (written by the submitters)
The effectiveness of the seasonal influenza vaccine varies between individuals. Specific risk groups with comorbidities, such as the obese, have an increased risk of infection even when vaccinated. It has been proposed that a heightened baseline inflammatory state and alterations in adaptive immune cell populations in obese individuals may adversely impact immune response to pathogens and vaccines.
Read the full summary ↓
Therefore, understanding differences in vaccine response in obese individuals is critical for the development of improved influenza vaccine design and strategies. Previously, we identified a transcriptomic signature prior to seasonal influenza vaccination that is predictive of an individual’s response to the influenza vaccine. To understand the dynamics of the host response following vaccination we studied systemic gene expression from whole blood collected from 163 vaccinated individuals on days 3, 7, and 28 post-vaccination. Gene expression profiles were compared between high and low vaccine responders in both obese and non-obese groups. We detected characteristic changes in gene expression over time, with a peak at day 7 post-vaccination. A large subset of genes associated with the adaptive immune response exhibited significantly different expression in high- and non- vaccine responders. Distinct gene sets presented differing temporal patterns in different weight and response groups, indicative of molecular processes impacting the immune response to vaccination.
Published in
Obese individuals exhibit distinct temporal gene expression dynamics in response to influenza vaccination
Hockman M, Matthews J, Carlock MA et al. · Microbiology spectrum 2025 · PMID 40548708 · doi:10.1128/spectrum.03354-24
This dataset
Open GSE271520 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 GSE271520_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 PRJNA1132158 and SRA study SRP518151. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40548708) ↗
Study design
163 × blood, Day 3, UGA4, vs 163 × blood, Day 7, UGA4, vs 74 × blood, Day 28, UGA4,

Supports a between-group comparison across 400 samples.

How we read this: 3 replicated groups read from the first 400 of 489 sample titles; they account for 400 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

+ 449 more — browse all 489 samples with per-sample file links →

Datasets on a similar topic

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