GEO series

Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumonia

GSE288215 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/10/21 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × Lung, HCoV-OC43, Csf2rb KO, vs 3 × Lung, PBS, Csf2rb KO, vs 3 × Lung, HCoV-OC43, WT, vs 3 × Lung, PBS, WT,Groups 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: Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumoniaCell reports · 2025

Summary (written by the submitters)

Seasonal coronaviruses, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), only cause severe respiratory symptoms in a small fraction of infected individuals. However, the host factors that determine the variable responses to coronavirus infection remain unclear. Here, we use seasonal human coronavirus OC43 (HCoV-OC43) infection as an asymptomatic model that triggers both innate and adaptive immune responses in mice.

Read the full summary ↓

Interestingly, innate sensing pathways as well as adaptive immune cells are not essential in protection against HCoV-OC43. Instead, alveolar macrophage (AMΦ) deficiency in mice results in COVID-19-like severe pneumonia post HCoV-OC43 infection, with abundant neutrophil infiltration, neutrophil extracellular trap (NET) release, and exaggerated pro-inflammatory cytokine production. Mechanistically, AMΦ efficiently phagocytose HCoV-OC43, effectively blocking virus spread, whereas, in their absence, HCoV-OC43 triggers Toll-like receptor (TLR)-dependent chemokine production to cause pneumonia. These findings reveal the central role of AMΦ in defending against seasonal HCoV-OC43 with clinical implications for human immunopathology associated with coronavirus infection.

Published in

Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumonia

Zhong X, Xie T, Wang SY et al. · Cell reports 2025 · PMID 40222012 · doi:10.1016/j.celrep.2025.115531

This dataset

Open GSE288215 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 GSE288215_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 PRJNA1216573 and SRA study SRP560371. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40222012) ↗

Study design

3 × Lung, HCoV-OC43, Csf2rb KO, vs 3 × Lung, PBS, Csf2rb KO, vs 3 × Lung, HCoV-OC43, WT, vs 3 × Lung, PBS, WT,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8761366 Lung, HCoV-OC43, Csf2rb KO, rep1 Lung, HCoV-OC43, Csf2rb…
GSM8761367 Lung, HCoV-OC43, Csf2rb KO, rep2 Lung, HCoV-OC43, Csf2rb…
GSM8761368 Lung, HCoV-OC43, Csf2rb KO, rep3 Lung, HCoV-OC43, Csf2rb…
GSM8761369 Lung, PBS, Csf2rb KO, rep1 Lung, PBS, Csf2rb KO,
GSM8761370 Lung, PBS, Csf2rb KO, rep2 Lung, PBS, Csf2rb KO,
GSM8761371 Lung, PBS, Csf2rb KO, rep3 Lung, PBS, Csf2rb KO,
GSM8761372 Lung, HCoV-OC43, WT, rep1 Lung, HCoV-OC43, WT,
GSM8761373 Lung, HCoV-OC43, WT, rep2 Lung, HCoV-OC43, WT,
GSM8761374 Lung, HCoV-OC43, WT, rep3 Lung, HCoV-OC43, WT,
GSM8761375 Lung, PBS, WT, rep1 Lung, PBS, WT,
GSM8761376 Lung, PBS, WT, rep2 Lung, PBS, WT,
GSM8761377 Lung, PBS, WT, rep3 Lung, PBS, WT,

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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.