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Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

GSE299043 Homo sapiens (human) RNA-seq (gene expression) 654 samples Submitted 2025/06/06 Platform GPL18573Platform GPL24676Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 654 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
654 samples: 27 conditions, mostly with about 16 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
Multimodal profiling reveals tissue-directed signatures of human immune cells altered with ageNature immunology · 2025
Summary (written by the submitters)
The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years.
Read the full summary ↓
We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.
Published in
Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age
Wells SB, Rainbow DB, Mark M et al. · Nature immunology 2025 · PMID 40804529 · doi:10.1038/s41590-025-02241-4
This dataset
Open GSE299043 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 GSE299043_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 PRJNA1215450 and SRA study SRP559768. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40804529) ↗
Study design
27 conditions, mostly with about 16 replicates each
D496_002_ADT_CZINY ×16 D496_002_GEX_CZINY ×16 D496_002_HTO_CZINY ×16 D503_001_ADT_CZINY ×16 D503_001_GEX_CZINY ×16 D503_001_HTO_CZINY ×16 D512_001_ADT_CZINY ×16 D512_001_GEX_CZINY ×16 +19 more

Supports a between-group comparison across 400 samples.

How we read this: 27 replicated groups read from the first 400 of 654 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

+ 614 more — browse all 654 samples with per-sample file links →

Datasets on a similar topic

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