GEO series

Macrophage-intrinsic and IL-9-dependent arginine metabolism promotes lung tumor growth

GSE292222 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2026/03/17 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 25 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: 25 samples: 8 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.

Summary (written by the submitters)

Tumor-associated macrophages are an abundant, tumor-infiltrating cell population that supports the evasion of tumor cells from anti-tumoral immune cell detection by generating an immunosuppressive tumor-immune microenvironment (TIME). The immunosuppressive function of macrophages is dictated by the cytokine environment. IL-9 is a pleiotropic cytokine that can be a positive or negative regulator of tumor growth.

Read the full summary ↓

Our lab previously identified a pro-tumoral role of IL-9 by expanding lung interstitial macrophage populations and inducing the expression of arginase 1 (ARG1) to enhance tumor growth. However, the underlying mechanism by which IL-9R/ARG1+ interstitial macrophages promote tumor progression remains incomplete. Here, we demonstrate that macrophage-targeting nanoparticles containing Arg1 siRNA can therapeutically reduce tumor burden and reduce pro-tumor arginine-derived metabolite production. Furthermore, using bulk RNA sequencing of lung macrophages isolated from Il9r-/-:WT mixed-bone marrow chimeric mice, we demonstrate that IL-9 intrinsically alters the transcriptomic landscape of lung interstitial macrophages. Mechanistically, IL-9 promotes intrinsic Arg1 expression through an IRF4-dependent regulatory pathway and modulates arginine and polyamine concentration within interstitial macrophages and lung tissue, resulting in increased lung tumor growth and altered macrophage phenotypes. Thus, our work defines a pro-tumor mechanism of IL-9-responsive macrophages mediated by altered intrinsic arginine metabolism in lung interstitial macrophages that enhances lung tumor growth.

This dataset

Open GSE292222 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 GSE292222_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 PRJNA1237503 and SRA study SRP573995. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in duplicate

IL9RKO Tumor CD11C- KO ×3 IL9RKO Tumor CD11C+ KO ×3 ARG1CKO Tumor CD11C- CKO ×3 IL9RKO Tumor CD11C- WT ×2 IL9RKO Tumor CD11C+ WT ×2 ARG1CKO Tumor CD11C- WT ×2 ARG1CKO Tumor CD11C+ WT ×2 ARG1CKO Tumor CD11C+ CKO ×2 +6 more

Supports a case/control comparison: 12 samples read as cases, 2 as controls.

How we read this: 8 replicated groups read from 25 sample titles; they account for 19 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

GSM8853368 WT:ARG1 naïve WT 1
GSM8853369 WT:ARG1 naïve ARG1 CKO 1
GSM8853370 WT:IL9RKO naïve WT 1
GSM8853371 WT:IL9RKO naïve IL9RKO 1
GSM8853372 WT:IL9RKO Tumor CD11C- WT 1 IL9RKO Tumor CD11C- WT
GSM8853373 WT:IL9RKO Tumor CD11C- WT 2 IL9RKO Tumor CD11C- WT
GSM8853374 WT:IL9RKO Tumor CD11C+ WT 1 IL9RKO Tumor CD11C+ WT
GSM8853375 WT:IL9RKO Tumor CD11C+ WT 2 IL9RKO Tumor CD11C+ WT
GSM8853376 WT:IL9RKO Tumor CD11C- KO1 IL9RKO Tumor CD11C- KO
GSM8853377 WT:IL9RKO Tumor CD11C- KO2 IL9RKO Tumor CD11C- KO
GSM8853378 WT:IL9RKO Tumor CD11C- KO3 IL9RKO Tumor CD11C- KO
GSM8853379 WT:IL9RKO Tumor CD11C+ KO1 IL9RKO Tumor CD11C+ KO
GSM8853380 WT:IL9RKO Tumor CD11C+ KO2 IL9RKO Tumor CD11C+ KO
GSM8853381 WT:IL9RKO Tumor CD11C+ KO3 IL9RKO Tumor CD11C+ KO
GSM8853382 WT:ARG1CKO Tumor CD11C- WT1 ARG1CKO Tumor CD11C- WT
GSM8853383 WT:ARG1CKO Tumor CD11C- WT2 ARG1CKO Tumor CD11C- WT
GSM8853384 WT:ARG1CKO TumorCD11C- WT3
GSM8853385 WT:ARG1CKO Tumor CD11C+WT1
GSM8853386 WT:ARG1CKO Tumor CD11C+ WT2 ARG1CKO Tumor CD11C+ WT
GSM8853387 WT:ARG1CKO Tumor CD11C+ WT3 ARG1CKO Tumor CD11C+ WT
GSM8853388 WT:ARG1CKO Tumor CD11C- CKO 1 ARG1CKO Tumor CD11C- CKO
GSM8853389 WT:ARG1CKO Tumor CD11C- CKO2 ARG1CKO Tumor CD11C- CKO
GSM8853390 WT:ARG1CKO Tumor CD11C- CKO 3 ARG1CKO Tumor CD11C- CKO
GSM8853391 WT:ARG1CKO Tumor CD11C+ CKO1 ARG1CKO Tumor CD11C+ CKO
GSM8853392 WT:ARG1CKO Tumor CD11C+ CKO2 ARG1CKO Tumor CD11C+ CKO

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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.