Table 1.
Summary of the published gene expression datasets on SARS‐CoV‐2 infection analyzed in this study.
| Dataset name a | Sample type | Sample size b | Platform | Reference |
|---|---|---|---|---|
| Vero | Vero E6 cell line | 6 | Bulk RNA‐seq | Riva et al (2020) |
| NHBE | Primary normal human bronchial epithelial cell | 6 | Bulk RNA‐seq | Blanco‐Melo et al (2020) |
| A549 | A549 human lung adenocarcinoma cell line with exogenous ACE2 expression | 6 | Bulk RNA‐seq | Blanco‐Melo et al (2020) |
| Calu‐3 | Calu‐3 human lung adenocarcinoma cell line | 6 | Bulk RNA‐seq | Blanco‐Melo et al (2020) |
| 293T | HEK293T human embryonic kidney cell line | 12 | Bulk RNA‐seq | Weingarten‐Gabby et al (2021) |
| Caco‐2 | Caco‐2 human colorectal adenocarcinoma cell line | 6 | MS‐based proteomics | Bojkova et al (2020b) |
| Swab.Butler | NP swab samples from human individuals | 580 | Bulk RNA‐seq | Butler et al (2021) |
| Swab.Lieberman | NP swab samples from human individuals | 484 | Bulk RNA‐seq | Lieberman et al (2020) |
| BALF | BALF from human individuals | 6 | Bulk RNA‐seq | Xiong et al (2020b) |
| SC.Liao | BALF from human individuals (epithelial cells were used in analysis) | 13 | scRNA‐seq | Liao et al (2020) |
| SC.Chua.Basal | NP and bronchial samples from human individuals (basal cells were used in analysis) | 24 | scRNA‐seq | Chua et al (2020) |
| SC.Chua.Ciliated | NP and bronchial samples from human individuals (ciliated cells were used in analysis) | 24 | scRNA‐seq | Chua et al (2020) |
BALF, bronchoalveolar lavage fluid; MS, mass spectrometry; NP, nasopharyngeal; RNA‐seq, RNA‐sequencing; scRNA‐seq, single‐cell RNA‐sequencing.
a
These are the names used in figure labels throughout the text.
b
The total number of replicates (virus‐infected and control combined) used for analysis in in vitro datasets, or the total number of human individuals (patients and controls combined) used for analysis in in vivo datasets. In some datasets, only a subset of all the available samples were analyzed.