Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome
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SciScore for 10.1101/2021.06.06.447293: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources S1 to S11 Tables S1 to S6 Cell culture and virus infection: HEK293T (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, HEK293Tsuggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)3111C0001CCC000091), Huh-7 (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, 3111C0001CCC000679), Calu-3 (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, 3111C0001CCC000032), … SciScore for 10.1101/2021.06.06.447293: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources S1 to S11 Tables S1 to S6 Cell culture and virus infection: HEK293T (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, HEK293Tsuggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)3111C0001CCC000091), Huh-7 (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, 3111C0001CCC000679), Calu-3 (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, 3111C0001CCC000032), Cos-7 (Kunming Cell Bank, Chinese Academy of Sciences, 3153C0001000000037) and MA-104 (Chinese Typical Culture Preservation Center Cell Bank, 3142C0001000000041) cells were cultured in DMEM (ThermoFisher,0030034DJ) supplemented with 10% fetal bovine serum (Gibco, 10099-141C) and penicillin-streptomycin (ThermoFisher,15140122) at 37°C, 5% CO2. Huh-7suggested: NoneSoftware and Algorithms Sentences Resources Bioinformatics analysis of whole genome sequencing data: Reads from whole genome sequencing data were mapped to human genome plus SARS-CoV-2 genome by using BWA (version 0.7.17)3, and genome coverage statistics was obtained by samtools (version 1.12)4. BWAsuggested: (BWA, RRID:SCR_010910)samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Chimeric gene analysis: Chimeric reads between host and SARS-CoV-2 were obtained via the above STAR analysis pipeline. STARsuggested: (STAR, RRID:SCR_004463)For these reads, the fragments from host genome were annotated by corresponding genome annotation reference by bedtools intersectBed6. bedtoolssuggested: (BEDTools, RRID:SCR_006646)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.
Results from scite Reference Check: We found no unreliable references.
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