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. 2023 May 5;19(5):e1011050. doi: 10.1371/journal.pcbi.1011050

Table 1. RNA-sequencing datasets used as inputs for network-based drug predictions.

Dataset Source Public Identifier/Link Sample Source Tissue/Cell Type Conditions assessed for predictions COVID-19 samples Control samples Drugs predicted
Greninger 17 GSE152075 Nasal swab samples from COVID patients Nasopharyngeal COVID > healthy 430 54 377
Mertz 18 GSE151764 Autopsy samples from COVID patients Lung COVID > healthy 16 6 623
Mertz 18 GSE151764 Autopsy samples from COVID patients Lung COVID (patients w/ normal BMI) > healthy 2 6 647
Mertz 18 GSE151764 Autopsy samples from COVID patients Lung COVID (patients w/ high BMI) > healthy 14 6 571
OSF https://osf.io/7nrd3/ COVID patients Blood PBMC COVID > healthy 3 3 330
OSF https://osf.io/7nrd3/ COVID patients Bronchoalveolar lavage fluid COVID > healthy 32 54 436
Redmond 16 GSE151803 Organoids Liver SARS-CoV-2 infected > mock treated 6 6 810
Redmond 16 GSE151803 Organoids Pancreas SARS-CoV-2 infected > mock treated 3 3 393
Svendsen 19 GSE150392 Human induced pluripotent stem cell-derived cells Cardiomyocytes SARS-CoV-2 infected > mock treated 3 3 716
Takayama 14 GSE150819 Organoids Bronchial epithelial cells SARS-CoV-2 infected > mock treated 3 3 719
tenOever 20 GSE147507 Cultured cells infected with SARS-CoV-2 A549 SARS-CoV-2 infected > mock treated 3 3 480
tenOever 20 GSE147507 Autopsy samples COVID patients Lung COVID > healthy 2 2 576
tenOever 20 GSE147507 & GSE200074 Autopsy samples COVID patients Lung COVID > healthy 2 2 711
Ting 15 GSE150316 Autopsy samples from COVID patients Lung COVID > healthy 52 5 384