SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery

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1. Version published to 10.1016/j.celrep.2021.109055

   May 1, 2021
2. 

   ScreenIT

   Jul 2, 2020

   SciScore for 10.1101/2020.06.29.174623: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Human lung tissue was obtained from deceased organ donors in compliance with consent procedures developed by International Institute for the Advancement of Medicine (IIAM) and approved by the Internal Review Board at Cedar-Sinai Medical Center. IRB: Human lung tissue was obtained from deceased organ donors in compliance with consent procedures developed by International Institute for the Advancement of Medicine (IIAM) and approved by the Internal Review Board at Cedar-Sinai Medical Center.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   SciScore for 10.1101/2020.06.29.174623: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Human lung tissue was obtained from deceased organ donors in compliance with consent procedures developed by International Institute for the Advancement of Medicine (IIAM) and approved by the Internal Review Board at Cedar-Sinai Medical Center. IRB: Human lung tissue was obtained from deceased organ donors in compliance with consent procedures developed by International Institute for the Advancement of Medicine (IIAM) and approved by the Internal Review Board at Cedar-Sinai Medical Center.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Viable epithelial cells were further enriched by fluorescence associated cell sorting (FACS) using DAPI (Thermo Fisher Scientific) and antibodies against EPCAM (CD326), CD45 and CD31 (Biolegend) on a BD Influx cell sorter (Becton Dickinson).	antibodies against EPCAM (CD326) suggested: (Abgent Cat# AM1102a, RRID:AB_2231180) CD45 suggested: None CD31 suggested: None
   The following primary antibodies were used: Acetylated tubulin (1:200, Sigma Aldrich, Cat. No. T6793); Mucin 5AC, 45M1 (1:500, Thermo Fisher Scientific, Cat. No. MA5-12178); HTII-280 (1:500, Terrace Biotech, Cat. No. TB-27AHT2-280); SARS-CoV-2 spike (S) protein (1:100, BEI Resources NR-616 Monoclonal Anti-SARS-CoV S Protein (Similar to 240C) SARS coronavirus); Cleaved caspase-3 (1:200, Cell Signaling Technology Cat. No. 9661).	Acetylated tubulin suggested: (Sigma-Aldrich Cat# T6793, RRID:AB_477585) Anti-SARS-CoV S Protein suggested: None Cleaved caspase-3 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Vero-E6 cells were cultured in Eagle’s minimal essential medium (MEM) (Corning) supplemented with 10% fetal bovine serum (Corning), penicillin-streptomycin (100 units/ml, Gibco), 2 mM L-glutamine (Gibco) and 10 mM HEPES (Gibco).	Vero-E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Samples were mounted using Fluoromount G (Thermo Fisher Scientific), imaged on a Zeiss LSM 780 Confocal Microscope and images were processed using Zen Blue software (Zeiss).	Zen Blue suggested: (ZEN Digital Imaging for Light Microscopy, RRID:SCR_013672)
   Raw reads were aligned using Star aligner 2.6.1 (8)/RSEM 1.2.28 (9) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation with SARS-Cov2 virus genome MT246667.1 https://www.ncbi.nlm.nih.gov/nuccore/MT246667.1.	Star suggested: (STAR, RRID:SCR_004463) http://www.gencodegenes.org suggested: (HapMap 3 and ENCODE 3, RRID:SCR_004563) GENCODE suggested: (GENCODE, RRID:SCR_014966)
   Differential gene expression was determined by DESeq2 (10).	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   Pathway analysis was performed using Ingenuity Pathway Analysis. Statistics: Statistical analysis was performed using GraphPad Prism version 8 software.	Ingenuity Pathway Analysis suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653) GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results 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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 19 and 21. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   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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3. 

   Version published to 10.1101/2020.06.29.174623 on bioRxiv

   Jun 29, 2020