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Antibiotics and Immune Responses study

GSE198276 Homo sapiens (human) RNA-seq (gene expression) 326 samples Submitted 2025/01/14 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 326 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
326 samples: 326 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
Bifidobacteria support optimal infant vaccine responsesNature · 2025
Summary (written by the submitters)
Blood collected from infants at week 6 and week 7 of life to profile how the transcriptome is changed following routine early life vaccination. Paired faecal metagenomic data is available for these infants under BioProject PRJNA807448 at the Sequence Read Archive.
Published in
Bifidobacteria support optimal infant vaccine responses
Ryan FJ, Clarke M, Lynn MA et al. · Nature 2025 · PMID 40175554 · doi:10.1038/s41586-025-08796-4
This dataset
Open GSE198276 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 GSE198276_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 PRJNA814322 and SRA study SRP363268. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40175554) ↗
Study design
326 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 326 sample titles: 326 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

+ 286 more — browse all 326 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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.