Lung expression of genes putatively involved in SARS-CoV-2 infection is modulated in cis by germline variants

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1. Version published to 10.1038/s41431-021-00831-y

   Mar 1, 2021
2. 

   ScreenIT

   Jun 25, 2020

   SciScore for 10.1101/2020.06.24.168534: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Raw data were log2-transformed and normalized using the robust spline normalization method implemented in the lumi Bioconductor package [24].	lumi suggested: (lumi, RRID:SCR_012781)
   After pre-processing, measured intensities for genes of interest were extracted and then merged after adjusting for batch effects using the ComBat function from the sva R Bioconductor package [	ComBat suggested: (ComBat, RRID:SCR_010974) Bioconductor suggested: (Bioconductor, RRID:SCR_006442)
   Genotype data were subjected to quality control using PLINK v1.90b6.16 [26] following the protocol described in [27].	PLINK sugges…

   SciScore for 10.1101/2020.06.24.168534: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Raw data were log2-transformed and normalized using the robust spline normalization method implemented in the lumi Bioconductor package [24].	lumi suggested: (lumi, RRID:SCR_012781)
   After pre-processing, measured intensities for genes of interest were extracted and then merged after adjusting for batch effects using the ComBat function from the sva R Bioconductor package [	ComBat suggested: (ComBat, RRID:SCR_010974) Bioconductor suggested: (Bioconductor, RRID:SCR_006442)
   Genotype data were subjected to quality control using PLINK v1.90b6.16 [26] following the protocol described in [27].	PLINK suggested: (PLINK, RRID:SCR_001757)
   The resulting dataset was then converted to a tabular format with the option --recode A-transpose. eQTL analyses: To test whether gene expression in lung tissue varied with the genotype of SNPs, we carried out an eQTL analysis by standard additive linear regression model, using the MatrixEQTL package [28] in R environment, assuming that genotype has an additive effect on gene expression.	MatrixEQTL suggested: None
   Linkage disequilibrium data and minor allele frequencies in the different populations were retrieved from the Ensembl genome browser.	Ensembl genome browser suggested: (Ensembl Genome Browser, RRID:SCR_013367)

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   Results from OddPub: Thank you for sharing your data.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   Version published to 10.1101/2020.06.24.168534v1 on bioRxiv

   Jun 24, 2020