A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity
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SciScore for 10.1101/2021.10.27.466206: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by the Ethical Committee of Clinical Investigation of Galicia (CEIC ref.
Consent: Written informed consent was obtained for subjects before study inclusion.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources After isolation, RNA amount and integrity was checked using TapeStation 4200 (Agilent), and DV200 values were calculated to both ensure that >50% of the of the RNA fragments were above 200nt and estimate the optimal sample input for the nCounter analysis. Agilentsuggested: (Agilent Bravo NGS, RRID:SCR_019473)The GeNorm algorithm (38) … SciScore for 10.1101/2021.10.27.466206: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by the Ethical Committee of Clinical Investigation of Galicia (CEIC ref.
Consent: Written informed consent was obtained for subjects before study inclusion.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources After isolation, RNA amount and integrity was checked using TapeStation 4200 (Agilent), and DV200 values were calculated to both ensure that >50% of the of the RNA fragments were above 200nt and estimate the optimal sample input for the nCounter analysis. Agilentsuggested: (Agilent Bravo NGS, RRID:SCR_019473)The GeNorm algorithm (38) implemented in the R package CrtlGene (39) was used to test for the most stable and optimal number of genes for normalization. GeNormsuggested: (geNORM, RRID:SCR_006763)Data normalization was performed through a combined approach using both DESeq2 (40) and RUVSeq (41) as described in (42). DESeq2suggested: (DESeq, RRID:SCR_000154)Volcano plots and heatmaps were built with EnhancedVolcano (43) and ComplexHeatmap (44) R packages, respectively. ComplexHeatmapsuggested: (ComplexHeatmap, RRID:SCR_017270)All graphics were created using R (www.r-project.org) software and the ggplot2 package (45). ggplot2suggested: (ggplot2, RRID:SCR_014601)For GSEA we used all available molecular measurements (log2FC) from the genes included in the DE to detect coordinated changes in the expression of genes from same pathway. GSEAsuggested: (SeqGSEA, RRID:SCR_005724)Analyses were carried out using the Clusterprofiler (47) R package. Clusterprofilersuggested: (clusterProfiler, RRID:SCR_016884)We tested both the GO (Gene Ontology) and Reactome databases. Reactomesuggested: (Reactome, RRID:SCR_003485)Microarray and RNA-seq data were downloaded from the public gene expression microarray repository Gene Expression Omnibus (GEO) under accession numbers: GSE64456 (49), GSE40012 (50), GSE42026 (51), GSE60244 (52), those also included in Thair et al. (23) as viral cohorts; and GSE72829 (53), GSE69529 (54). Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Next, we used Limma package (59) to detect DEG and calculate log2FC values between groups. Limmasuggested: (LIMMA, RRID:SCR_010943)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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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