Table 1. Origins of human and mouse gene expression datasets.
| Study name | Species | Dataset source | Infected Tissue | Control Tissue | Method | Platform | Re-analyzed | Notes |
|---|---|---|---|---|---|---|---|---|
| Winkler 2, 4 & 7 dpi |
Mouse (K18-hACE2) |
PRJNA645133 | SARS-CoV-2 infected lung | Mock infected lung | RNA-Seq (poly-A selected) |
Illumina NovaSeq 6000 | Y | 2.5x104 p.f.u. n = 4–6 per group |
| Suhrbier 2 & 4 dpi |
Mouse (K18-hACE2) |
PRJNA767499 PRJEB43658 |
SARS-CoV-2 infected lung | Mock infected lung | RNA-Seq (poly-A selected) | Illumina NextSeq 550 | Y | 5x104 CCID50 n = 4–6 per group |
| mACE2-hACE2 2, 4, 6 & 10 dpi |
Mouse (mACE2-hACE2) |
PRJNA767499 | SARS-CoV-2 infected lung | Mock infected lung | RNA-Seq (poly-A selected) |
Illumina NextSeq 550 | Y | 5x104 CCID50 n = 3/4 per group |
| Mouse adapted virus, MA1 4 dpi |
Mouse C57BL/6J |
PRJNA804321 | SARS-CoV-2 infected lung | Mock infected lung | RNA-Seq (poly-A selected) |
Illumina NextSeq 550 | N | 5x104 CCID50 n = 5 per group |
| Wu | Human | PRJNA646224 | Formalin fixed paraffin embedded post mortem COVID-19 lung | Formalin fixed paraffin embedded healthy tissue from lung cancer patients | RNA-Seq (rRNA-depleted) |
Illumina NextSeq 550 |
Y | Infected n = 9, Control n = 10. Medicated. |
| Alfi | Human | PRJNA688321 | SARS-Cov-2 infected Ex vivo 3D lung organ culture | mock infected Ex vivo 3D lung organ culture | RNA-Seq (poly-A selected) |
Illumina NextSeq 500 | Y | Infected n = 10 Control n = 10 |
| Blanco-Melo | Human | PRJNA615032 | Formalin fixed COVID-19 post-mortem lung | Healthy post-surgery lung biopsy | RNA-Seq (poly-A selected) |
Illumina NextSeq 500 |
N | Infected n = 2 Control n = 2 4 RNA-Seq libraries for each. |
| Acker-mann | Human | Vivli Center for Clinical Research Data | Formalin fixed COVID-19 post-mortem lung | Formalin fixed healthy donated lung | Nano-String | nCounter Inflamma-tion Panel | N | Infected n = 7, Control n = 10 Alveolar damage noted |
K18-hACE2 mouse studies from two independent laboratories provided five data sets from lungs of SARS-CoV-2-infected K18-hACE2 mice. K18-hACE2 data covered three time points, specifically, days post infection (dpi). Four mACE2-hACE2 datasets were generated from lungs of SARS-CoV-2-infected mACE2-hACE2 mice, and covered four time points. The previously published MA1 dataset was derived from lungs of C57BL/6J mice infected with the MA1 mouse-adapted strain of SARS-CoV-2. Four independent human studies provided three gene expression datasets from SARS-CoV-2-infected lungs, and one from 3D lung organ culture infected ex vivo with SARS-CoV-2. The Ackerman study analyzed expression of 249 mRNAs associated with inflammation. All infections were with SARS-CoV-2 isolates belonging to the original or ancestral lineage. PRJ prefixed annotations represent NCBI Bioproject accession numbers. Reanalysis means raw fastq files were re-analyzed for this study using STAR, RSEM and EdgeR.