Common Genetic Variation in Humans Impacts In Vitro Susceptibility to SARS-CoV-2 Infection
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SciScore for 10.1101/2020.09.20.300574: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable All wildtype and shRNA experiments in lung alveolosphere cells, as well as all CRISPR-engineered AA and GG experiments were conducted in NSB3113 (female, 18 years old, European descent) and NSB3188 (female, 14 years old, European descent) (Schrode et al., 2019). Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Lentivirus generation: Third-generation VSV.G pseudotyped HIV-1 lentiviruses were produced by polyethylenimine (PEI, Polysciences #23966-2)-transfection of HEK293T cells and packaged with … SciScore for 10.1101/2020.09.20.300574: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable All wildtype and shRNA experiments in lung alveolosphere cells, as well as all CRISPR-engineered AA and GG experiments were conducted in NSB3113 (female, 18 years old, European descent) and NSB3188 (female, 14 years old, European descent) (Schrode et al., 2019). Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Lentivirus generation: Third-generation VSV.G pseudotyped HIV-1 lentiviruses were produced by polyethylenimine (PEI, Polysciences #23966-2)-transfection of HEK293T cells and packaged with VSVG-coats using established methods. HEK293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)SARS-CoV-2 was propagated in Vero E6 cells in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES. Vero E6suggested: RRID:CVCL_XD71)Software and Algorithms Sentences Resources Reads were aligned to Mesocricetus auratus Ensembl MesAur1.0 using STAR aligner, and mappid using CustomDESeq2. STARsuggested: (STAR, RRID:SCR_015899)Differential expression analysis was performed using edgeR (v3.26.8) (Robinson et al., 2010), limma (v3.40.6) (Ritchie et al., 2015) and Glimma (v1.12.0) (Su et al., 2017) packages. edgeRsuggested: (edgeR, RRID:SCR_012802)limmasuggested: (LIMMA, RRID:SCR_010943)Glimmasuggested: (Glimma, RRID:SCR_017389)Enrichment analysis was performed using WebGestaltR (0.4.4) using custom neural gene sets of interest (Schrode et al., 2019) and interferon gene sets (Blanco-Melo et al., 2020). WebGestaltRsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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: No clinical trial numbers were referenced.
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.
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