A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits
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SciScore for 10.1101/2020.07.29.20163949: (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 Cells were lysed on ice for 25 min with a QSonica CL-18 sonicator operating at 40% power (15 s on, 45 s off). Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources A panel of reactions was performed in which various templates were used: synthetic SARS-CoV-2 RNA (ATCC #VR-3276SD), HEK293T cell RNA (containing RNase P RNA) generated in-house by TRIzol (Invitrogen #15596026) extraction of HEK293T cells grown to 60% confluency, a mixture of SARS-CoV-2 RNA and HEK293T cell RNA, nuclease-free water … SciScore for 10.1101/2020.07.29.20163949: (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 Cells were lysed on ice for 25 min with a QSonica CL-18 sonicator operating at 40% power (15 s on, 45 s off). Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources A panel of reactions was performed in which various templates were used: synthetic SARS-CoV-2 RNA (ATCC #VR-3276SD), HEK293T cell RNA (containing RNase P RNA) generated in-house by TRIzol (Invitrogen #15596026) extraction of HEK293T cells grown to 60% confluency, a mixture of SARS-CoV-2 RNA and HEK293T cell RNA, nuclease-free water (negative, no template control), or SARS-CoV-2 plasmid (2019-nCoV_N_Positive Control, IDT #10006625, 10,000-50,000 copies/rxn). HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources Multiplex assay interpretation: A MATLAB script (https://github.com/rmannino3/COVID19DataAnalysis) was written to interpret the results of RT-qPCR assays conducted with GT multiplexed (FAM/HEX) primers and probes based on 96-well data exported from QuantStudio 6 and StepOne Plus qPCR instruments. MATLABsuggested: (MATLAB, RRID:SCR_001622)Inhibition of RNase A by GT-rRI was assessed by adapting a published method (54), namely, monitoring a reduction in RNase A (Thermo Fisher Scientific# EN0531)-catalyzed hydrolysis of 1 mM cytidine 2’:3’-cyclic monophosphate (cCMP) (Sigma # C9630) in 100 mM Tris-acetate, pH 6.5, 1 mM EDTA, 5 mM DTT at room temperature. Thermo Fisher Scientific#suggested: 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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