Synthetic lethality-based prediction of anti-SARS-CoV-2 targets
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SciScore for 10.1101/2021.09.14.460408: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Cells were then incubated for 2 h at room temperature with primary anti-SARS-CoV-2 N protein rabbit polyclonal antibody (kind gift from Dr. Adolfo Garcia-Sastre), followed by three PBS washes and 1 h incubation with Alexa Fluor 488-conjugated anti-rabbit secondary antibody (A-11008, ThermoFisher) diluted in 3% BSA. anti-SARS-CoV-2 N proteinsuggested: Noneanti-rabbitsuggested: (Molecular Probes Cat# A-11008, RRID:AB_143165)Experimental Models: Cell Lines Sentences Resources Differential expression analysis of transcriptomic data on SARS-CoV-2 infection: Several RNA-sequencing datasets of … SciScore for 10.1101/2021.09.14.460408: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Cells were then incubated for 2 h at room temperature with primary anti-SARS-CoV-2 N protein rabbit polyclonal antibody (kind gift from Dr. Adolfo Garcia-Sastre), followed by three PBS washes and 1 h incubation with Alexa Fluor 488-conjugated anti-rabbit secondary antibody (A-11008, ThermoFisher) diluted in 3% BSA. anti-SARS-CoV-2 N proteinsuggested: Noneanti-rabbitsuggested: (Molecular Probes Cat# A-11008, RRID:AB_143165)Experimental Models: Cell Lines Sentences Resources Differential expression analysis of transcriptomic data on SARS-CoV-2 infection: Several RNA-sequencing datasets of SARS-CoV-2-infected and matched control samples were obtained as follows: Vero E6 cells (Riva et al. 2020; from the GEO database, dataset ID GSE153940), A549 cells with exogenous ACE2 (A549ACE2; Blanco-Melo et al. 2020; from GEO, GSE147507), nasopharyngeal swab samples from human COVID-19 patients (Butler et al. 2020 and Lieberman et al. 2020, from the Supplementary Materials of the respective publications), single-cell data of nasopharyngeal and bronchial samples from COVID-19 patients (Chua et al. 2020; from FigShare https://doi.org/10.6084/m9.figshare.12436517), and single-cell data of bronchoalveolar lavage fluid from COVID-19 patients (Liao et al. 2020; obtained following instructions in https://github.com/zhangzlab/covid_balf). A549suggested: NoneFor the Vero E6 and A549ACE2 data, we performed differential expression (DE) analysis of virus-infected vs control samples with the DESeq2 R package (Love et al. 2014). Vero E6suggested: NoneCalculation of weighted DE score: Each of 140 candidates have the same or different significant DE genes from six different transcriptomic datasets - in vitro Vero E6 (Riva et al. 2020), in vitro A549ACE2 cells (Blanco-Melo et al. 2020), two in vivo Bulk Swab datasets (Butler et al. 2020 and Lieberman et al. 2020) and two in vivo single-cell RNA-seq datasets (Chua et al. 2020 and Liao et al. 2020). A549ACE2suggested: NoneTargeted siRNA screen: Screen: To evaluate the effect of the 26 predicted targets on viral replication and cell viability, a targeted siRNA screen was conducted using human Caco-2 cells (ATCC) Caco-2suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025)Software and Algorithms Sentences Resources Differential expression analysis of transcriptomic data on SARS-CoV-2 infection: Several RNA-sequencing datasets of SARS-CoV-2-infected and matched control samples were obtained as follows: Vero E6 cells (Riva et al. 2020; from the GEO database, dataset ID GSE153940), A549 cells with exogenous ACE2 (A549ACE2; Blanco-Melo et al. 2020; from GEO, GSE147507), nasopharyngeal swab samples from human COVID-19 patients (Butler et al. 2020 and Lieberman et al. 2020, from the Supplementary Materials of the respective publications), single-cell data of nasopharyngeal and bronchial samples from COVID-19 patients (Chua et al. 2020; from FigShare https://doi.org/10.6084/m9.figshare.12436517), and single-cell data of bronchoalveolar lavage fluid from COVID-19 patients (Liao et al. 2020; obtained following instructions in https://github.com/zhangzlab/covid_balf). FigSharesuggested: (FigShare, RRID:SCR_004328)For the Vero E6 and A549ACE2 data, we performed differential expression (DE) analysis of virus-infected vs control samples with the DESeq2 R package (Love et al. 2014). DESeq2suggested: (DESeq, RRID:SCR_000154)Annotation of the final SL-based candidate target gene list: The predicted targets (140 candidates) were mapped to known drugs (clinically approved and experimental/ investigational) that target (i.e. inhibit) them using drug target annotation from DrugBank (Wishart et al. 2018). DrugBanksuggested: (DrugBank, RRID:SCR_002700)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04518735 Completed Evolution of COVID-19 in Anticoagulated or Antiaggregated Pa… NCT04844658 Recruiting Covid-19, Hospitalized, PatIents, Nasafytol NCT04578158 Completed Trial to Study the Adjuvant Benefits of Quercetin Phytosome … NCT04377789 Completed Effect of Quercetin on Prophylaxis and Treatment of COVID-19 Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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