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Development of an ideal inactivated vaccine for COVID-19 (mouse lung RNA-seq data)

GSE270151 Mus musculus (mouse) RNA-seq (gene expression) 52 samples Submitted 2026/03/31 Platform GPL28330

At a glance

RNA-seq (gene expression) · mouse · 52 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: 52 samples: 11 conditions, mostly with about 5 replicates eachGroups 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)

Since the emergence of coronavirus disease 2019 (COVID-19), there has been a continuous threat to human health. Whole particle virus vaccine (WPV) for COVID-19 has been developed because of its potency, safety, and handling easiness, however, it has been recognized that it is difficult to maintain the particle structure. Here, we established the preparation method for intact COVID-19 WPV that retains the virus particle structure, including spike proteins on the surface, by improving the culture condition and purification process.

Read the full summary ↓

The effectiveness of the prepared vaccines, intact and non-intact WPV without surface spike proteins, was examined in a mouse model. A single dose of intact WPV effectively induced humoral immunity compared to non-intact WPV, as indicated by higher titers of neutralization antibodies. Both vaccines significantly induced immune responses to suppress virus replication in the lungs. However, more severe vascular damage with massive immune cell infiltration in the vascular smooth muscle cell layer was observed in the lungs of mice vaccinated with non-intact WPV. These results indicate the importance of the structural integrity of WPV in inducing effective and protective immunity. These findings provide significant insight into the development of COVID-19 WPV for practical use.

This dataset

Open GSE270151 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 GSE270151_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 PRJNA1125346 and SRA study SRP514653. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

11 conditions, mostly with about 5 replicates each

FC-WPV_1μg, 3dpi, ×5 FC-WPV_5μg, 3dpi, ×5 CF-WPV_1μg, 3dpi, ×5 CF-WPV_5μg, 3dpi, ×5 FC-WPV_1μg, 10dpi, ×5 FC-WPV_5μg, 10dpi, ×5 CF-WPV_1μg, 10dpi, ×5 CF-WPV_5μg, 10dpi, ×5 +3 more

Supports a between-group comparison across 52 samples.

How we read this: 11 replicated groups read from 52 sample titles; they account for 52 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

GSM8335592 unvaccinated, 3dpi, rep1 unvaccinated, 3dpi,
GSM8335593 unvaccinated, 3dpi, rep2 unvaccinated, 3dpi,
GSM8335594 unvaccinated, 3dpi, rep3 unvaccinated, 3dpi,
GSM8335595 unvaccinated, 3dpi, rep4 unvaccinated, 3dpi,
GSM8335596 FC-WPV_1μg, 3dpi, rep1 FC-WPV_1μg, 3dpi,
GSM8335597 FC-WPV_1μg, 3dpi, rep2 FC-WPV_1μg, 3dpi,
GSM8335598 FC-WPV_1μg, 3dpi, rep3 FC-WPV_1μg, 3dpi,
GSM8335599 FC-WPV_1μg, 3dpi, rep4 FC-WPV_1μg, 3dpi,
GSM8335600 FC-WPV_1μg, 3dpi, rep5 FC-WPV_1μg, 3dpi,
GSM8335601 FC-WPV_5μg, 3dpi, rep1 FC-WPV_5μg, 3dpi,
GSM8335602 FC-WPV_5μg, 3dpi, rep2 FC-WPV_5μg, 3dpi,
GSM8335603 FC-WPV_5μg, 3dpi, rep3 FC-WPV_5μg, 3dpi,
GSM8335604 FC-WPV_5μg, 3dpi, rep4 FC-WPV_5μg, 3dpi,
GSM8335605 FC-WPV_5μg, 3dpi, rep5 FC-WPV_5μg, 3dpi,
GSM8335606 CF-WPV_1μg, 3dpi, rep1 CF-WPV_1μg, 3dpi,
GSM8335607 CF-WPV_1μg, 3dpi, rep2 CF-WPV_1μg, 3dpi,
GSM8335608 CF-WPV_1μg, 3dpi, rep3 CF-WPV_1μg, 3dpi,
GSM8335609 CF-WPV_1μg, 3dpi, rep4 CF-WPV_1μg, 3dpi,
GSM8335610 CF-WPV_1μg, 3dpi, rep5 CF-WPV_1μg, 3dpi,
GSM8335611 CF-WPV_5μg, 3dpi, rep1 CF-WPV_5μg, 3dpi,
GSM8335612 CF-WPV_5μg, 3dpi, rep2 CF-WPV_5μg, 3dpi,
GSM8335613 CF-WPV_5μg, 3dpi, rep3 CF-WPV_5μg, 3dpi,
GSM8335614 CF-WPV_5μg, 3dpi, rep4 CF-WPV_5μg, 3dpi,
GSM8335615 CF-WPV_5μg, 3dpi, rep5 CF-WPV_5μg, 3dpi,
GSM8335616 unvaccinated, 10dpi, rep1 unvaccinated, 10dpi,
GSM8335617 unvaccinated, 10dpi, rep2 unvaccinated, 10dpi,
GSM8335618 unvaccinated, 10dpi, rep3 unvaccinated, 10dpi,
GSM8335619 unvaccinated, 10dpi, rep4 unvaccinated, 10dpi,
GSM8335620 FC-WPV_1μg, 10dpi, rep1 FC-WPV_1μg, 10dpi,
GSM8335621 FC-WPV_1μg, 10dpi, rep2 FC-WPV_1μg, 10dpi,
GSM8335622 FC-WPV_1μg, 10dpi, rep3 FC-WPV_1μg, 10dpi,
GSM8335623 FC-WPV_1μg, 10dpi, rep4 FC-WPV_1μg, 10dpi,
GSM8335624 FC-WPV_1μg, 10dpi, rep5 FC-WPV_1μg, 10dpi,
GSM8335625 FC-WPV_5μg, 10dpi, rep1 FC-WPV_5μg, 10dpi,
GSM8335626 FC-WPV_5μg, 10dpi, rep2 FC-WPV_5μg, 10dpi,
GSM8335627 FC-WPV_5μg, 10dpi, rep3 FC-WPV_5μg, 10dpi,
GSM8335628 FC-WPV_5μg, 10dpi, rep4 FC-WPV_5μg, 10dpi,
GSM8335629 FC-WPV_5μg, 10dpi, rep5 FC-WPV_5μg, 10dpi,
GSM8335630 CF-WPV_1μg, 10dpi, rep1 CF-WPV_1μg, 10dpi,
GSM8335631 CF-WPV_1μg, 10dpi, rep2 CF-WPV_1μg, 10dpi,

+ 12 more — browse all 52 samples with per-sample file links →

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Search all mouse RNA-seq datasets in GEO →

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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.