SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease
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SciScore for 10.1101/2020.05.09.20096511: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Owing to ethical considerations, privacy protection concerns, and to avoid identifying individual study participants in vulnerable populations, the Institutional Review Board of the National Institute of Diabetes and Digestive and Kidney Diseases has stipulated that individual-level gene expression and genotype data from the American Indian DKD study cannot be made publicly available. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Overlap of differentially expressed ACE2+ co-regulated … SciScore for 10.1101/2020.05.09.20096511: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Owing to ethical considerations, privacy protection concerns, and to avoid identifying individual study participants in vulnerable populations, the Institutional Review Board of the National Institute of Diabetes and Digestive and Kidney Diseases has stipulated that individual-level gene expression and genotype data from the American Indian DKD study cannot be made publicly available. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Overlap of differentially expressed ACE2+ co-regulated gene signatures with SARS-CoV-2 relevant gene sets: SARS-CoV-2 relevant gene sets were compiled from multiple published sources: 1) Bojkova_proteome is a list of differentially expressed proteins in Caco-2 cell line following SARS-Cov-2 infection (p < 0.05 at any time point)37 2) Gordon_interactome is a set of host proteins identified as physically interacting with SARS-CoV-2 viral proteins in HEK-293T cells36; 3) Zhou_interactome is a literature-curated list of genes related to diverse coronaviruses20; 4) Blanco-Melo_NHBE is a list of differentially regulated genes in response to SARS-CoV-2 infection in normal human bronchial epithelial cells39. Caco-2suggested: NoneHEK-293Tsuggested: NoneSoftware and Algorithms Sentences Resources The output from the sequencer was first processed by CellRanger, the proprietary 10X Chromium single cell gene expression analysis software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-rangersuggested: (Cell Ranger , RRID:SCR_017344)For cell type annotation we used publicly available resources including published literature, Kidney Interactive Transcriptome (http://humphreyslab.com/SingleCell/), Human Protein Atlas (HPA) (https://www.proteinatlas.org), the Epithelial Systems Biology Laboratory (ESBL) (https://hpcwebapps.cit.nih.gov/ESBL/Database/), scRNAseq data and Immgen (https://www.immgen.org/). https://www.proteinatlas.orgsuggested: (HPA, RRID:SCR_006710)Functional network analysis: To determine the biological processes and pathways in the ACE2+ differentially expressed gene sets, we performed functional network clustering in the PTEC gene functional network derived from GIANT 2.032, 33 This network was generated through regularized Bayesian integration of 61,400 publicly available expression, physical interaction and other omics experiments to generate a fully connected weighted graph representing functional relationships in biological pathways in PTEC. GIANTsuggested: NoneA dynamic user-friendly interface at HumanBase (hb.flatironinstitute.org/covid-kidney) is available for researchers to explore the functional networks of gene expression signatures. HumanBasesuggested: (HumanBase, RRID:SCR_016145)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 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.
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