The Architecture of SARS-CoV-2 Transcriptome
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SciScore for 10.1101/2020.03.12.988865: (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 Nanopore direct RNA sequencing: For nanopore sequencing on non-infected and SARS-CoV-2-infected Vero cells, each 4 μg of DNase I (Takara)-treated total RNA in 8 μl was used for library preparation following the manufacturer’s instruction (the Oxford Nanopore DRS protocol, SQK-RNA002) with minor adaptations. Verosuggested: NoneSoftware and Algorithms Sentences Resources Templates for in vitro transcription were prepared by PCR (Q5® … SciScore for 10.1101/2020.03.12.988865: (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 Nanopore direct RNA sequencing: For nanopore sequencing on non-infected and SARS-CoV-2-infected Vero cells, each 4 μg of DNase I (Takara)-treated total RNA in 8 μl was used for library preparation following the manufacturer’s instruction (the Oxford Nanopore DRS protocol, SQK-RNA002) with minor adaptations. Verosuggested: NoneSoftware and Algorithms Sentences Resources Templates for in vitro transcription were prepared by PCR (Q5® High-Fidelity DNA Polymerase [NEB]) with virus-specific PCR primers followed by in vitro transcription (MEGAscript™ T7 Transcription Kit [Invitrogen]). MEGAscript™suggested: NoneThe library was loaded on FLO-MIN106D flow cell followed by 42 hours sequencing run on MinION device (Oxford Nanopore Technologies). MinIONsuggested: (MinION, RRID:SCR_017985)The sequence reads were aligned to the reference sequence database composed of the C. sabaeus genome (ENSEMBL release 99), a SARS-CoV-2 genome, yeast ENO2 cDNA (YHR174W), and human ribosomal DNA complete repeat unit (GenBank U13369.1) using minimap2 2.17 (Li, 2018) with options “-k 13 -x splice -N 32 -un”. ENSEMBLsuggested: (Ensembl, RRID:SCR_002344)We used STAR (Dobin et al., 2013) with many switches to completely turn off the penalties of non-canonical eukaryotic splicing: “--outFilterType BySJout -- outFilterMultimapNmax 20 --alignSJoverhangMin 8 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --scoreGapNoncan -4 --scoreGapATAC -4 --chimOutType WithinBAM HardClip --chimScoreJunctionNonGTAG 0 --alignSJstitchMismatchNmax -1 -1 -1 -1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000”. STARsuggested: (STAR, RRID:SCR_015899)Results from OddPub: Thank you for sharing your 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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