← BioTransfer GEO Dataset Finder
GEO series

Fibroblast orchestration of inflammaging via NF-kB activation (Lung Resident CD45+ cell and fibroblast analysis)

GSE285880 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2025/12/04 Platform GPL24247Platform GPL34290Platform GPL17021
At a glance

Single-cell RNA-seq · mouse · 24 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
24 samples: 6 conditions, mostly with about 4 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
Fibroblast orchestration of inflammaging via NF-kB activationbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
In this study we used scRNA-sequencing to compare lung resident CD45+ cells and bulk RNA-sequencing to compare lung PDGFRa+ fibroblasts from 2-month-old mice in which the NF-kB inhibitor Tnfaip3 has been deleted from fibroblasts (D1cA20) with control mice (A20control). We identified enrichment of Gzmk+CD8+ T cells in the D1cA20 relative to control mice.
Read the full summary ↓
As a follow-up to this initial study we used bulk RNA sequencing to compare the transcriptomes of lung adventitial fibroblasts from 4-month C57BL/6 (Young B6), 21-month C57BL/6 (Aged B6), 4-month Tnfaip3 f/f (Tnfaip3 Control) and 4-month Dermo1-cre;Tnfaip3f/f (Tnfaip3 CKO/D1cA20) mice. We identified that aged B6 adventitial fibroblasts share transcriptional similarity with those from young Tnfaip3 CKO mice. Pathway analysis revealed NF-kB to be significantly upregulated in both Aged B6 and Tnfaip3 CKO relative to Young B6 or Tnfaip3 control.
Published in
Fibroblast orchestration of inflammaging via NF-kB activation
Allen NC, Ringler C, Lee JY et al. · bioRxiv : the preprint server for biology 2025 · PMID 41256682 · doi:10.1101/2025.10.01.679697
This dataset
Open GSE285880 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 GSE285880_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1206702 and SRA study SRP555540. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41256682) ↗
Study design
6 conditions, mostly with about 4 replicates each
Lung adventitial fibroblasts from young Tnfai… ×4 Lung adventitial fibroblasts from young Dermo… ×4 Lung adventitial fibroblasts from young B6 mo… ×4 Lung adventitial fibroblasts from aged B6 mou… ×4 PDGFRA+ lung fibroblasts from Tnfaip3f/f mouse ×3 PDGFRA+ lung fibroblasts from Dermo1-cre/+;Tn… ×3 Lung resident CD45+ cells from Tnfaip3f/f (A2… ×1 Lung resident CD45+ cells from Dermo1-cre/+;T… ×1

Supports a between-group comparison across 22 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 22 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
Datasets on a similar topic

Search all mouse 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.