A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors
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SciScore for 10.1101/2020.05.08.084806: (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. Table 2: Resources
Software and Algorithms Sentences Resources Resulting reads were mapped to the human genome (hg19) using STAR (https://github.com/alexdobin/STAR) with defined settings, i.e. --alignIntronMin 20 --alignIntronMax 1000000 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outFilterMultimapNmax 20, and only uniquely mapped reads were considered for the calculation of expression. STARsuggested: (STAR, RRID:SCR_015899)https://github.com/alexdobin/STARsuggested: (Hamilton Microlab STAR Automated Liquid Handling, RRID:SCR_019993)RP… SciScore for 10.1101/2020.05.08.084806: (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. Table 2: Resources
Software and Algorithms Sentences Resources Resulting reads were mapped to the human genome (hg19) using STAR (https://github.com/alexdobin/STAR) with defined settings, i.e. --alignIntronMin 20 --alignIntronMax 1000000 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outFilterMultimapNmax 20, and only uniquely mapped reads were considered for the calculation of expression. STARsuggested: (STAR, RRID:SCR_015899)https://github.com/alexdobin/STARsuggested: (Hamilton Microlab STAR Automated Liquid Handling, RRID:SCR_019993)RPKM was calculated using bamutils (http://ngsutils.org/modules/bamutils/count/) for individual genes annotated in the human RefSeq database. RefSeqsuggested: (RefSeq, RRID:SCR_003496)Cross-species analysis: Trimmed mean of M values (TMM) normalized cross-species Counts per million (CPM) values were imported in R and variable features were identified using “FindVariableFeatures” function implemented in the Seurat package using mean.var.plot (mvp) as a selection method. Seuratsuggested: (SEURAT, RRID:SCR_007322)Results 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 55. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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