Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples
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Abstract
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SciScore for 10.1101/2020.08.04.20167874: (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 not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources RT PCR (FP_1, R) and a second round of PCR (FP_2, R) was performed on HEK293T lysate for construction of an in vitro RPP30 standard DNA template. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources We also tested 1x Tween with Qiagen Protease and RNA Secure (ThermoFisher), which also works but resulted in more sample-to-sample variability and required additional incubation steps. ThermoFishersuggested: (ThermoFisher; SL 8; …SciScore for 10.1101/2020.08.04.20167874: (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 not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources RT PCR (FP_1, R) and a second round of PCR (FP_2, R) was performed on HEK293T lysate for construction of an in vitro RPP30 standard DNA template. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources We also tested 1x Tween with Qiagen Protease and RNA Secure (ThermoFisher), which also works but resulted in more sample-to-sample variability and required additional incubation steps. ThermoFishersuggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)Purified RNA was quantified and library quality was assessed using the Agilent TapeStation. Agilent TapeStationsuggested: (Agilent TapeStation Laptop, RRID:SCR_019547)On the NextSeq550 and MiniSeq, the post-run wash was performed automatically by the instruments, and no human intervention was required. MiniSeqsuggested: NoneFor this application, the MiSeq and MiniSeq (Rapid Run Kit) require 2 custom sequencing primer mixes, the Read1 primer mix and the i7 primer mix. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Analysis: The bioinformatic analysis consists of standard conversion of BCL files into FASTQ sequencing files using Illumina’s bcl2fastq software (v2.20.0.422). Illumina’ssuggested: Nonebcl2fastqsuggested: (bcl2fastq , RRID:SCR_015058)In this analysis we make use of a few custom scripts written in R that rely on the ShortRead 30 and stringdist 31 packages for processing fastq files and calculating hamming distances between observed and expected amplicons and indices. ShortReadsuggested: (ShortRead, RRID:SCR_006813)Results from OddPub: Thank you for sharing your code and data.
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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