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Chemokine receptor expression patterns delineate distinct interstitial macrophage subsets in the lung and define a trajectory from monocytes to mature macrophages, bulk RNA-sequencing data

GSE306514 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/05/27 Platform GPL30172
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
Chemokine receptor expression defines a trajectory from monocytes to mature macrophages in the lungJournal of leukocyte biology · 2026
Summary (written by the submitters)
Inflammatory chemokine receptors CCR1, CCR2 and CCR5 are critical for directing recruitment of monocytes and macrophages in the context of inflammation. However, the discrete role for each receptor in monocyte/macrophage biology remains poorly understood, with previous reports citing receptor redundancy. Here, we have used transcriptomic approaches to examine inflammatory chemokine receptor expression on lung interstitial macrophage populations.
Read the full summary ↓
We have demonstrated that interstitial macrophages can be divided into three distinct subsets, each of which express specific patterns of chemokine receptors, and that there are dynamic changes in chemokine receptor expression as macrophages differentiate from monocytes in the lung. Furthermore, macrophages expressing different combinations of chemokine receptors are transcriptionally distinct from one another, suggesting non-redundant functions for CCR 1, 2 and 5. Finally, we examined changes in macrophage chemokine receptor expression in vitro after treatment with varied TLR ligands, and show that CCR1 is specifically increased in response to bacterial but not viral ligands. Our data provide compelling evidence that macrophage chemokine receptor expression is not redundant, but specific and maleable in response to discrete inflammatory stimuli.
Published in
Chemokine receptor expression defines a trajectory from monocytes to mature macrophages in the lung
Mathie H, Medina-Ruiz L, Schuette F et al. · Journal of leukocyte biology 2026 · PMID 42087270 · doi:10.1093/jleuko/qiag059
This dataset
Open GSE306514 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 GSE306514_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 PRJNA1311020 and SRA study SRP613066. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42087270) ↗
Study design
8 conditions, mostly in triplicate
MHCII_hi_macrophage, CCR1+ CCR2+ CCR5+, ×3 MHCII_hi_macrophage, CCR1+ CCR5+, ×3 MHCII_hi_macrophage, CCR2+ CCR5+, ×3 MHCII_hi_macrophage, CCR5+, ×3 MHCII_lo macrophage, CCR1+ CCR5+, ×3 MHCII_lo_macrophage, CCR2+, ×3 MHCII_lo_macrophage, CCR5+, ×3 MHCII_lo_macrophage, No iCCRs, ×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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