GEO series

Premature thymic involution in young Foxn1lacz mutant mice causes peripheral T cell phenotypes similar to aging-induced immunosenescence

GSE264402 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/03/21 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 11 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: Mus musculus (mouse)
Samples: 11 samples: 5 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: Insulin-like growth factor 2 as a driving force for exponential expansion and differentiation of the neonatal thymusDevelopment (Cambridge, England) · 2025

Summary (written by the submitters)

The thymus is a primary lymphoid organ generating self-restricted and self-tolerant naïve T-cells. Early in life the thymus starts to involute, resulting in decreased naïve T-cell output which may be more self-reactive, leading to an increased prevalence of autoimmunity. A decrease in the transcription factor FOXN1 is an early event in thymic involution.

Read the full summary ↓

Using the Foxn1lacz model, we studied how premature thymic involution affects the thymic microenvironment, thymocytes, and peripheral T cell immunity. We found that early thymic involution led to aged-like thymic epithelial cells that resulted in aged-like thymocyte phenotypes, with a significant decrease in CD4+ single-positive T-cells. We also observed severe lymphopenia in Foxn1lacz mice caused by the premature decrease in T-cell production, resulting in a peripheral T-cell phenotype similar to de novo aged peripheral T-cells. Moreover, following T cell receptor stimulation, Foxn1lacz peripheral T cells had reduced IL-2 secretion and strong initial IFN-g responses, resembling aged wild-type peripheral T-cell responses. Lastly, influenza response in Foxn1lacz had a reduction in some aspects of T cell responses to influenza infection, similar to thymectomized mice. Our study shows an independent and direct impact of premature thymic involution on both thymopoiesis and peripheral immune niches likely contributing to immunosenescence and inflammaging as observed in the elderly population.

Published in

Insulin-like growth factor 2 as a driving force for exponential expansion and differentiation of the neonatal thymus

Kang SW, Helm BR, Wang Y et al. · Development (Cambridge, England) 2025 · PMID 40110795 · doi:10.1242/dev.204347

This dataset

Open GSE264402 in finder → Find more mouse 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 GSE264402_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 PRJNA1102343 and SRA study SRP502850. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40110795) ↗

Study design

5 conditions, mostly in duplicate

Stroma_1mo_ZZ ×3 Stroma_1mo_WT ×2 Splenocyte_1mo_WT ×2 Splenocyte_1mo_ZZ ×2 Splenocyte_18mo_WT ×2

Supports a between-group comparison across 11 samples.

How we read this: 5 replicated groups read from 11 sample titles; they account for 11 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

GSM8217634 Stroma_1mo_WT_1 Stroma_1mo_WT
GSM8217635 Stroma_1mo_WT_2 Stroma_1mo_WT
GSM8217636 Stroma_1mo_ZZ_1 Stroma_1mo_ZZ
GSM8217637 Stroma_1mo_ZZ_2 Stroma_1mo_ZZ
GSM8217638 Stroma_1mo_ZZ_3 Stroma_1mo_ZZ
GSM8217639 Splenocyte_1mo_WT_1 Splenocyte_1mo_WT
GSM8217640 Splenocyte_1mo_WT_2 Splenocyte_1mo_WT
GSM8217641 Splenocyte_1mo_ZZ_1 Splenocyte_1mo_ZZ
GSM8217642 Splenocyte_1mo_ZZ_2 Splenocyte_1mo_ZZ
GSM8217643 Splenocyte_18mo_WT_1 Splenocyte_18mo_WT
GSM8217644 Splenocyte_18mo_WT_2 Splenocyte_18mo_WT

Datasets on a similar topic

GSE315892 RNA-binding proteins Zfp36l1 and Zfp36l2 protect against premature thymic involution. 1 samples shares involution, premature
GSE249752 Age-related epithelial defects limit thymic function and regeneration [single cell; Foxn1LacZ] 4 samples shares foxn1lacz
GSE62762 Aging-induced type I interferon response at the choroid plexus negatively affects brain function. 75 samples shares aging-induced
GSE271324 METTL3 governs thymocyte development and thymic involution by regulating ferroptosis 35 samples shares involution
GSE243187 METTL3 dictates the development of thymocytes via restraining ferroptosis program during age related thymic involution 16 samples shares involution
GSE285005 Induction of Senescence During Postpartum Mammary Gland Involution supports tissue remodeling and promotes postpartum tumorigenesis 12 samples shares involution
GSE280678 Ferroptosis Mediated by the IDO1/Kyn/AhR Pathway Triggers Acute Thymic Involution in Sepsis 8 samples shares involution
GSE275466 Study title: B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters - B and T Cell Singlet and PIC Single Cell RNA Seq 6 samples shares immunosenescence

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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.