Transcriptional profiling of lungs from SARS-CoV-2-infected K18-hACE2 mice
RNA-seq (gene expression) · mouse · 15 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
- 15 samples: 15 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.
- Paper
- Redundant and distinct mechanisms suppress innate immune activation during SARS-CoV-2 infectionPLoS biology · 2026
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE254969_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1072723 and SRA study SRP487819. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 8 samples read as cases, 7 as controls.
How we read this: Read from 15 sample titles: 15 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.
- GSM8061494 L, mock
- GSM8061495 1, mock
- GSM8061496 2, mock
- GSM8061497 3, mock
- GSM8061498 L, wt SARS-CoV-2
- GSM8061499 R, wt SARS-CoV-2
- GSM8061500 N, wt SARS-CoV-2
- GSM8061501 L, vNSP1 mutant
- GSM8061502 R, vNSP1 mutant
- GSM8061503 N, vNSP1 mutant
- GSM8061504 RR, vNSP1 mutant
- GSM8061505 L, vNSP15 mutant
- GSM8061506 R, vNSP15 mutant
- GSM8061507 N, vNSP15 mutant
- GSM8061508 RR, vNSP15 mutant
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- GSE263891 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs 6072 samples shares lungs
- GSE313869 Impact of Fc engineering on the transcriptional profile of monocytes and interstitial macrophages in the lungs of Hu-FcgR Tg mice after MA30 infection 36 samples shares lungs
- GSE294560 Bulk RNAseq profiling of Streptococcus pneumoniae EF3030 and Influenza A virus (A/California/07/2009(H1N1)) mono/coinfection in the mouse lungs. 60 samples shares lungs
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares lungs
- GSE230597 Bulk RNA-seq of ILC2, Tconv, Th2, Treg Gata3hi and Treg Gatalo from the lungs of IL-33 treated mice 22 samples shares lungs
- GSE326909 scRNAseq Dataset of lungs from WT and Clec1a KO mice following primary or secondary E. coli lung infection 12 samples shares lungs
- GSE279918 Gene expression profile at single cell level of lungs of adult male and female C57BL/6 mice with andwithout high-fat diet-induced obesity 12 samples shares lungs
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.