The SARS-CoV-2 RNA interactome

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   ScreenIT

   Nov 3, 2020

   SciScore for 10.1101/2020.11.02.364497: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Vero and HCT-8 cells were maintained in DMEM (Welgene) and RPMI 1640 (Welgene) respectively, both with 1X Antibiotic-Antimycotic (Gibco) and 10% FBS (Gibco) and cultured in CO2 incubator with 5% CO2 37 DC.	HCT-8 suggested: RRID:CVCL_5947)
   For SARS-CoV-2 infection, 7 ⍰ 106 Vero cells were plated in T-175 flasks 24 hours before infection.	Vero suggested: None
   For siRNA transfection, 3.5 ⍰ 105 Calu-3 cells, maintained in DMEM with 1X Antibiotic-Antimycotic and 10% FBS in CO2 incubator with 5% CO2 37 □C, were plated in 12 well plate and final 50 nM siRNAs were reverse-transfected using …

   SciScore for 10.1101/2020.11.02.364497: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Vero and HCT-8 cells were maintained in DMEM (Welgene) and RPMI 1640 (Welgene) respectively, both with 1X Antibiotic-Antimycotic (Gibco) and 10% FBS (Gibco) and cultured in CO2 incubator with 5% CO2 37 DC.	HCT-8 suggested: RRID:CVCL_5947)
   For SARS-CoV-2 infection, 7 ⍰ 106 Vero cells were plated in T-175 flasks 24 hours before infection.	Vero suggested: None
   For siRNA transfection, 3.5 ⍰ 105 Calu-3 cells, maintained in DMEM with 1X Antibiotic-Antimycotic and 10% FBS in CO2 incubator with 5% CO2 37 □C, were plated in 12 well plate and final 50 nM siRNAs were reverse-transfected using Lipofectamine RNAiMAX (Invitrogen) and ON-TARGETplus SMARTpool siRNAs (Horizon Discovery).	Calu-3 suggested: KCLB Cat# 30055, RRID:CVCL_0609)
   Software and Algorithms
   Sentences	Resources
   Preparation of antisense oligonucleotide templates: By scanning the genomic RNAs of SARS-CoV-2 (NCBI RefSeq accession NC_045512.2) and HCoV-OC43 (GenBank accession AY391777.1) from head to tail, partially overlapping 90 nt tiles were enumerated.	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Peptides from common contaminant proteins were identified by utilizing the contaminant database provided by MaxQuant.	MaxQuant suggested: (MaxQuant, RRID:SCR_014485)
   To improve the explanatory power of this analysis, we used the weight01 algorithm (Alexa et al., 2006) from the topGO R package which accounts for the GO graph structure and reduces local dependencies between GO terms.	topGO suggested: (topGO, RRID:SCR_014798)
   Detailed information of the Gene Ontology was from the GO.db R package (version 3.8.2), and GO gene annotations were from the org.	GO.db suggested: None
   Protein-protein interaction network analysis: We integrated protein-protein interaction data from the BioGRID database (Release 3.5.187) (Stark et al., 2006) and retrieved other proteins that do not necessarily bind to the SARS-CoV-2 RNA but form either transient or stable physical interactions with the host proteins identified from the RNP capture experiments.	BioGRID suggested: (BioGrid Australia, RRID:SCR_006334)
   Protein domain enrichment analysis: Pfam database (version 33.1) (El-Gebali et al., 2019) was used for protein domain enrichment analysis.	Pfam suggested: (Pfam, RRID:SCR_004726)

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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: We did not find any issues relating to colormaps.

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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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2. 

   Version published to 10.1101/2020.11.02.364497 on bioRxiv

   Nov 2, 2020