SARS-CoV-2 activates lung epithelial cell proinflammatory signaling and leads to immune dysregulation in COVID-19 patients
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SciScore for 10.1101/2020.05.08.20096024: (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
Experimental Models: Cell Lines Sentences Resources Bulk RNA-Seq data in three SARS-CoV-2 treated cell lines were also obtained for validation purpose, including primary human bronchial epithelial cells (NHBE), Calu-3 and A549-ACE2 (with vector expressing human ACE2)26. Calu-3suggested: NoneSoftware and Algorithms Sentences Resources All relevant data were downloaded from Gene Expression Omnibus under the accession number GSE122960, GSE145926 and GSE147507. scRNA-Seq data analysis: We re-analyzed the data from a count quantification matrix due to the un-available per-cell annotation. Gene Expression Omnibussuggested: (Gene Expression …SciScore for 10.1101/2020.05.08.20096024: (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
Experimental Models: Cell Lines Sentences Resources Bulk RNA-Seq data in three SARS-CoV-2 treated cell lines were also obtained for validation purpose, including primary human bronchial epithelial cells (NHBE), Calu-3 and A549-ACE2 (with vector expressing human ACE2)26. Calu-3suggested: NoneSoftware and Algorithms Sentences Resources All relevant data were downloaded from Gene Expression Omnibus under the accession number GSE122960, GSE145926 and GSE147507. scRNA-Seq data analysis: We re-analyzed the data from a count quantification matrix due to the un-available per-cell annotation. Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)High variable genes were determined using FindVariableFeatures in Seurat pipeline27. Seuratsuggested: (SEURAT, RRID:SCR_007322)Bulk RNA-Seq data analysis: RNA-seq reads were mapped onto the human reference (GRCh38 with gene annotations GENCODE v30) by HISAT2 (version 2.1.0) with the default options. HISAT2suggested: (HISAT2, RRID:SCR_015530)Gene expression levels were calculated as FPKM (Fragments per Kilobase of transcript per Million mapped reads) by rpkm method in edgeR. edgeRsuggested: (edgeR, RRID:SCR_012802)Differentially expressed genes (DEGs) were determined using DESeq2. DESeq2suggested: (DESeq, RRID:SCR_000154)We performed this method to uncover potential biological function shift under SARS-CoV-2 infection through mapping the molecules into known molecule sets by WebGestalt 29. WebGestaltsuggested: NoneTwo databases, KEGG and Reactome were used for canonical pathway detection. KEGGsuggested: (KEGG, RRID:SCR_012773)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 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: 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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