Table 1.
Summary of RNA-seq transcriptional profiling experiments. Data were taken from published experiments in which cell lines were inoculated with an infectious agent and compared to mock inoculations. Datasets were identified in the NCBI sequence read archive. Columns: Inf.-Mock: number of infected/mock samples in an experiment. ID: identifier used in this work. Abbreviations: DENV: Dengue virus; ECs: epithelial cells; hNEC: human nasal epithelial cells; MERS: Middle East Respiratory Syndrome Coronavirus; PBMC: Peripheral blood mononuclear cells; SARS: Severe acute respiratory syndrome-associated coronavirus. Strep: Streptococcus pneumoniae. RSV: Respiratory Syncytial Virus. The three datasets from SRP040070 were the high multiplicity of infection (MOI) experiments chosen from among a larger set of experiments. NSP1 (NSP2): SARS-CoV-2 NSP1 (NSP2) transfection 24 h.
| Sample | Cell line /Tissue | SRP | Inf.-Mock | Citation | ID |
|---|---|---|---|---|---|
| SARS (24 h) | MRC5 | SRP040070 | 6–3 | n/a | SARS |
| MERS (24 h) | MRC5 | SRP040070 | 3–3 | n/a | MERS-24 h |
| MERS (48 h) | MRC5 | SRP040070 | 3–3 | n/a | MERS-48 h |
| MERS (24 h) | Calu-3 | SRP227272 | 6–6 | [21] | MERS-Calu3 |
| Strep | Nasal ECs | SRP178454 | 5–8 | [22] | Strep |
| HCV (day 1) | Huh7.5.1 | SRP186406 | 3–3 | [23] | HCV |
| Zika | A549 | SRP251704 | 3–3 | [24] | Zika |
| DENV | A549 | SRP078309 | 3–3 | [9] | DENV |
| H3N2 | hNEC | SRP222569 | 10–8 | [25] | H3N2-NEC |
| H3N2 | lung | SRP216763 | 5–5 | [26] | H3N2-lung |
| RSV | Nasal Scrape | SRP273785 | 16–32 | n/a | RSV |
| SARS-CoV-2 inf. | SARS-CoV-2-A | n/a | 100–193 | [27] | SARS-COV-2-A |
| SARS-CoV-2 inf. | lung | SRP279203 | 5–5 | n/a | SARS-COV-2-B |
| SARS-CoV-2 inf. | Nasal ECs | SRP294125 | 3–3 | [28] | SARS-COV-2-C |
| NSP1 | HEK293 | SRP284977 | 3–3 | [29] | NSP1 |
| NSP2 | HEK293 | SRP284977 | 3–3 | [29] | NSP2 |