Characterization and functional interrogation of the SARS-CoV-2 RNA interactome
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SciScore for 10.1101/2021.03.23.436611: (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 not detected. Cell Line Authentication Contamination: All cell lines were periodically tested negative for mycoplasma contamination prior to use in experiments. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell lines: Lenti-X 293T cells (human embryonic kidney cells), A549 cells (Human alveolar basal epithelial carcinoma), and Vero E6 cells (African green monkey kidney cells) were maintained in Dulbecco Modified Eagle Medium (DMEM; Invitrogen Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% … SciScore for 10.1101/2021.03.23.436611: (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 not detected. Cell Line Authentication Contamination: All cell lines were periodically tested negative for mycoplasma contamination prior to use in experiments. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell lines: Lenti-X 293T cells (human embryonic kidney cells), A549 cells (Human alveolar basal epithelial carcinoma), and Vero E6 cells (African green monkey kidney cells) were maintained in Dulbecco Modified Eagle Medium (DMEM; Invitrogen Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) and 1% GlutaMAX (Life Technologies). Lenti-X 293Tsuggested: ATCC Cat# CRL-11270, RRID:CVCL_4401)Viruses titer was ascertained by plaque assays in Vero E6 cells and expressed as PFU per ml. Vero E6suggested: RRID:CVCL_XD71)293T cells stably expressing ACE2 were seeded at 9×106 cells per T150 flask (3 flasks per condition) and inoculated with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.001 or mock-treated. 293Tsuggested: NoneA549 cells stably expressing ACE2 were seeded in 24-well plate format (viral infection) or a 96-well plate (viability) and then were reverse transfected in duplicate with 30 nM of siRNA using the Lipofectamine RNAiMAX reagent (Invitrogen) according to manufacturer’s instruction. A549suggested: NoneSoftware and Algorithms Sentences Resources Cell populations were sorted based on GFP expression with a BD FACSAria II (Becton Dickinson) with FACSDiva 6.1.2 software (Becton FACSDivasuggested: (BD FACSDiva Software, RRID:SCR_001456)Acquisition was performed on an Attune NxT Flow Cytometer (Thermo Fisher Scientific) and analysis was done by using FlowJo software (Tree Star) Comprehensive identification of RNA binding proteins by mass spectrometry: ChIRP-M/S was performed as previously described by Ooi and colleagues (Ooi et al., 2019). FlowJosuggested: (FlowJo, RRID:SCR_008520)They were displayed together with the interacting-coronavirus proteins as an interaction network using Cytoscape (Shannon et al., 2003). Cytoscapesuggested: (Cytoscape, RRID:SCR_003032)This list of new interactors was analyzed with the Functional Annotation Tool of the online knowledge base DAVID Bioinformatics Resources 6.8, NIAID/NIH (Dennis et al., 2003) to identify statistical enrichments in KEGG pathway annotations (Kanehisa and Goto, 2000) KEGGsuggested: (KEGG, RRID:SCR_012773)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).
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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