GEO series

CCR10-Regulated Mucosal Immune Responses Support Restoration of Lung Tissue Homeostasis after SARS-CoV-2 infection.

GSE334311 Mus musculus (mouse) RNA-seq (gene expression) 9 samples Submitted 2026/08/07 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 9 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: 9 samples: 9 samples, each with a distinct title — no replicated groupsGroups 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)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. While most patients can clear the infection and recover, some develop severe symptoms associated with dysregulated immune activation that leads to injury of lungs. Clinical studies found that severities of COVID-19 patients correlated with levels of mucosa-homing CCR10+ immunoglobulin A (IgA) antibody-secreting cells (IgA-ASCs) while recovery was linked to expansion of CCR10+ type 2 innate lymphoid cells (ILC2s).

Read the full summary ↓

However, exact roles of CCR10-regulated mucosal immune responses in SARS-CoV-2 infection and pathology are not clear. Here, we addressed these questions using CCR10-knockout (KO) mice infected with a mouse-adapted strain of SARS-CoV-2. SARS-CoV-2-infected CCR10-KO mice had reduced IgA-ASCs but increased ILCs and T cells in lungs compared to control wild-type (WT) mice. However, CCR10-KO mice cleared SARS-CoV-2 as efficiently as WT mice, suggesting that CCR10-regulated mucosal immune responses are not critical for viral clearance. On the other hand, CCR10-KO mice, particularly males, were impaired in recovery from SARS-CoV-2-induced lung damages due to the immune dysregulation. Intranasal immunization overcame defective mucosal immune responses and prevented SARS-CoV-2-induced lung pathology in CCR10-KO mice. Our results revealed an important role of CCR10-regulated mucosal immune responses in restoration of lung homeostasis after SARS-CoV-2 infection.

This dataset

Open GSE334311 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 GSE334311_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 PRJNA1474577 and SRA study SRP706608. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 9 sample titles: 9 distinct titles with little repetition. 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

GSM9785249 CCR10 Het 1 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785250 CCR10 Het 2 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785251 CCR10 Het 3 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785252 CCR10 Het 4 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785253 CCR10 Het 5 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785254 CCR10 KO 6 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785255 CCR10 KO 7 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785256 CCR10 KO 9 Lung Tissue SARS-CoV-2 MA10 infected, Day 14
GSM9785257 CCR10 KO 10 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

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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.