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Heparan sulfate regulates amphiregulin programming of tissue reparative lung mesenchymal cells during influenza A virus infection in mice

GSE263616 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/02/05 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
Heparan sulfate regulates amphiregulin programming of tissue reparative lung mesenchymal cells during influenza A virus infection in miceNature communications · 2025
Summary (written by the submitters)
Amphiregulin is an immune cell-derived growth factor that plays critical roles in tissue repair. After influenza A infection, Treg cells in the lung produce amphiregulin, which signals to a specific Col14a1-expressing subpopulation of lung mesenchymal cells (Col14-LMC) to coordinate their repair activities towards the damaged lung epithelium.
Read the full summary ↓
Heparan sulfate is a subtype of proteoglycan that can be produced by all cells in the body, and has been implicated in altering growth factor signaling in numerous contexts. Amphiregulin has a heparan sulfate-binding domain; we sought to investigate how the inhibition of heparan sulfate on primary Col14-LMC affects their response to amphiregulin at the transcriptional level.
Published in
Heparan sulfate regulates amphiregulin programming of tissue reparative lung mesenchymal cells during influenza A virus infection in mice
Loffredo LF, Kustagi A, Ringham OR et al. · Nature communications 2025 · PMID 40032825 · doi:10.1038/s41467-025-57362-z
This dataset
Open GSE263616 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 GSE263616_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 PRJNA1098417 and SRA study SRP500639. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40032825) ↗
Study design
8 conditions, mostly in triplicate
Lung Col14-LMC, no HS inhibition, vehicle tre… ×3 Lung Col14-LMC, no HS inhibition, Areg 200 ng… ×3 Lung Col14-LMC, no HS inhibition, Areg 500 ng… ×3 Lung Col14-LMC, no HS inhibition, Areg 1000 n… ×3 Lung Col14-LMC, HS inhibition (NaClO3), vehic… ×3 Lung Col14-LMC, HS inhibition (NaClO3), Areg … ×3 Lung Col14-LMC, HS inhibition (NaClO3), Areg … ×3 Lung Col14-LMC, HS inhibition (NaClO3), Areg … ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
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