Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes
RNA-seq (gene expression) · mouse · 20 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
- 20 samples: 20 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
- Immune Signatures of SARS-CoV-2 Infection Resolution in Human Lung TissuesbioRxiv : the preprint server for biology · 2024
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 GSE255200_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 PRJNA1073929 and SRA study SRP488504. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 20 sample titles: 20 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.
- GSM8065665 Naïve, replicate A
- GSM8065666 Naïve, replicate B
- GSM8065667 Naïve, replicate C
- GSM8065668 Naïve, replicate D
- GSM8065669 2 dpi, replicate A
- GSM8065670 2 dpi, replicate B
- GSM8065671 12 dpi, replicate A
- GSM8065672 12 dpi, replicate B
- GSM8065673 Mouse #569, 12 dpi
- GSM8065674 Mouse #570, 2 dpi
- GSM8065675 Mouse #571, 12 dpi
- GSM8065676 Mouse #572, 2 dpi
- GSM8065677 Mouse #576, 2 dpi
- GSM8065678 Mouse #577, sample A, naive
- GSM8065679 Mouse #578, 12 dpi
- GSM8065680 Mouse #579, 2 dpi
- GSM8065681 Mouse #583, 12 dpi
- GSM8065682 Mouse #585, sample A, naive
- GSM8065683 Mouse #585, sample B, naive
- GSM8065684 Mouse #557, sample B, naive
- 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 sars-cov-2, monocytes, lung
- GSE260604 Ageing is Associated with an Insufficient Early Inflammatory Response of Lung Endothelial Cells in SARS-CoV-2 Infection 16 samples shares sars-cov-2, lung
- GSE315893 Characterization of Subchronic Lung and Brain Consequences Caused by Mouse-Adapted SARS-CoV-2 and Influenza A Infection of C57BL6 mice 44 samples shares sars-cov-2, lung
- GSE334311 CCR10-Regulated Mucosal Immune Responses Support Restoration of Lung Tissue Homeostasis after SARS-CoV-2 infection. 9 samples shares sars-cov-2, lung
- GSE329365 Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection [Lung4Day] 8 samples shares sars-cov-2, lung
- GSE254969 Transcriptional profiling of lungs from SARS-CoV-2-infected K18-hACE2 mice 15 samples shares sars-cov-2, lung
- GSE291215 Single-cell gene expression analysis using lung derived cells from SARS-CoV-2-infected mice in aged and adult mice 12 samples shares sars-cov-2, lung
- 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 monocytes, lung
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.