The pulmonary inflammatory microenvironment at the time of exposure governs innate control of SARS-CoV-2 replication
RNA-seq (gene expression) · mouse · 23 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
- 23 samples: 6 conditions, mostly with about 4 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.
- Paper
- The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replicationbioRxiv : 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 GSE254993_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 PRJNA1072986 and SRA study SRP487921. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 23 samples.
How we read this: 6 replicated groups read from 23 sample titles; they account for 23 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.
- GSM8061838 Lung, SCV2 + PBS ctrl 1 Lung, SCV2 + PBS ctrl
- GSM8061839 Lung, SCV2 + PBS ctrl 2 Lung, SCV2 + PBS ctrl
- GSM8061840 Lung, SCV2 + PBS ctrl 3 Lung, SCV2 + PBS ctrl
- GSM8061841 Lung, SCV2 + PBS ctrl 4 Lung, SCV2 + PBS ctrl
- GSM8061842 Lung, SCV2 + CpG 10ug i.ph one week prior to infection 1 Lung, SCV2 + CpG 10ug…
- GSM8061843 Lung, SCV2 + CpG 10ug i.ph one week prior to infection 2 Lung, SCV2 + CpG 10ug…
- GSM8061844 Lung, SCV2 + CpG 10ug i.ph one week prior to infection 3 Lung, SCV2 + CpG 10ug…
- GSM8061845 Lung, SCV2 + CpG 10ug i.ph one week prior to infection 4 Lung, SCV2 + CpG 10ug…
- GSM8061846 Lung, SCV2 + pam3CSK4 50ug i.ph one week prior to infection 1 Lung, SCV2 + pam3CSK4 …
- GSM8061847 Lung, SCV2 + pam3CSK4 50ug i.ph one week prior to infection 2 Lung, SCV2 + pam3CSK4 …
- GSM8061848 Lung, SCV2 + pam3CSK4 50ug i.ph one week prior to infection 3 Lung, SCV2 + pam3CSK4 …
- GSM8061849 Lung, SCV2 + pam3CSK4 50ug i.ph one week prior to infection 4 Lung, SCV2 + pam3CSK4 …
- GSM8061850 Lung, uninfected PBS ctrl 1 Lung, uninfected PBS ct…
- GSM8061851 Lung, uninfected PBS ctrl 2 Lung, uninfected PBS ct…
- GSM8061852 Lung, uninfected PBS ctrl 3 Lung, uninfected PBS ct…
- GSM8061853 Lung, uninfected CpG 10ug i.ph one week prior to infection 1 Lung, uninfected CpG 10…
- GSM8061854 Lung, uninfected CpG 10ug i.ph one week prior to infection 2 Lung, uninfected CpG 10…
- GSM8061855 Lung, uninfected CpG 10ug i.ph one week prior to infection 3 Lung, uninfected CpG 10…
- GSM8061856 Lung, uninfected CpG 10ug i.ph one week prior to infection 4 Lung, uninfected CpG 10…
- GSM8061857 Lung, uninfected pam3CSK4 50ug i.ph one week prior to infection 1 Lung, uninfected pam3CS…
- GSM8061858 Lung, uninfected pam3CSK4 50ug i.ph one week prior to infection 2 Lung, uninfected pam3CS…
- GSM8061859 Lung, uninfected pam3CSK4 50ug i.ph one week prior to infection 3 Lung, uninfected pam3CS…
- GSM8061860 Lung, uninfected pam3CSK4 50ug i.ph one week prior to infection 4 Lung, uninfected pam3CS…
- GSE305266 The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing 90 samples shares microenvironment, control
- GSE270016 Rejuvenation of aged oocyte through exposure to young follicular microenvironment 45 samples shares microenvironment, exposure
- GSE232854 Control of Mycobacterium abscessus pulmonary infection requires IFN- γ Induced formation of foam macrophages 22 samples shares pulmonary, control
- GSE341988 Sequential pathogen exposure normalizes the brain neuroimmune microenvironment and reveals a tissue-resident memory CD8 T cell-microglia axis shaping adult neurogenesis 8 samples shares microenvironment, exposure
- 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
- 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
- GSE282408 Non-apoptotic caspase-8 is critical for orchestrating exaggerated inflammation during severe SARS-CoV-2 infection 30 samples shares sars-cov-2
- GSE329370 Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection 26 samples shares sars-cov-2
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.