Single cell profiling in COVID-19 associated acute kidney injury reveals patterns of tubule injury and repair in human

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   ScreenIT

   Oct 8, 2021

   SciScore for 10.1101/2021.10.05.463150: (What is this?)

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

   Table 1: Rigor

   Ethics

   Consent: The consent was given orally by the next of kin, due to the ban on visits in force in our hospital. IACUC: The study was approved by the local ethical committee for human studies of Geneva, Switzerland (CCER 2020-00644, Commission Cantonale d’Ethique de la Recherche) and performed according to the Declaration of Helsinki principles. Euthanasia Agents: Briefly, 10- to 12-week-old, 25–28-g, male C57BL6/J or Six2TGC Rosa26rtTA pTREH2-GFP mice were anaesthetized with an intraperitoneal injection of ketamine/xylazine (ketamine, 105 mg kg–1; xylazine, 10 mg kg–1).

   Sex as a biological variable

   Briefly, 10- to 12-week-old, 25–28-g, male C57BL6/J or Six2TGC Rosa26rtTA pTREH2-GFP mice were …

   SciScore for 10.1101/2021.10.05.463150: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: The consent was given orally by the next of kin, due to the ban on visits in force in our hospital. IACUC: The study was approved by the local ethical committee for human studies of Geneva, Switzerland (CCER 2020-00644, Commission Cantonale d’Ethique de la Recherche) and performed according to the Declaration of Helsinki principles. Euthanasia Agents: Briefly, 10- to 12-week-old, 25–28-g, male C57BL6/J or Six2TGC Rosa26rtTA pTREH2-GFP mice were anaesthetized with an intraperitoneal injection of ketamine/xylazine (ketamine, 105 mg kg–1; xylazine, 10 mg kg–1).
   Sex as a biological variable	Briefly, 10- to 12-week-old, 25–28-g, male C57BL6/J or Six2TGC Rosa26rtTA pTREH2-GFP mice were anaesthetized with an intraperitoneal injection of ketamine/xylazine (ketamine, 105 mg kg–1; xylazine, 10 mg kg–1).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Immunochemistry staining were performed as followed: after antigen retrieval with pressurized heating chamber in citrate buffer pH7 or tris-EDTA pH9, 5 μm tissue sections were incubated with antibodies mouse monoclonal anti-human HAVCR1 (dilution 1:250, clone 219211, RD Systems), rabbit polyclonal anti-human PROM1 (dilution 1:250, Novus biological) and mouse monoclonal anti-human VCAM1 (dilution 1:25, clone 1.4C3, Invitrogen) for 1h at room temperature.	pH9 suggested: None anti-human HAVCR1 suggested: (R and D Systems Cat# FAB1750P, RRID:AB_10891505) anti-human PROM1 suggested: None anti-human VCAM1 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Briefly, 10- to 12-week-old, 25–28-g, male C57BL6/J or Six2TGC Rosa26rtTA pTREH2-GFP mice were anaesthetized with an intraperitoneal injection of ketamine/xylazine (ketamine, 105 mg kg–1; xylazine, 10 mg kg–1).	C57BL6/J suggested: None Rosa26rtTA pTREH2-GFP suggested: None
   Briefly, bilateral IRI was induced for 18 minutes in C57B6/J 8- to 10-wk-old male mice and body temperature was monitored and maintained at 36.5 to 37.5 °C throughout the procedure.	C57B6/J suggested: RRID:MGI:5818271)
   Recombinant DNA
   Sentences	Resources
   Briefly, 10- to 12-week-old, 25–28-g, male C57BL6/J or Six2TGC Rosa26rtTA pTREH2-GFP mice were anaesthetized with an intraperitoneal injection of ketamine/xylazine (ketamine, 105 mg kg–1; xylazine, 10 mg kg–1).	pTREH2-GFP suggested: None
   Software and Algorithms
   Sentences	Resources
   For each pattern cluster, pathway enrichment was performed using hypeR with a hypergeometric test and the REACTOME, KEGG, GOBP, WIKI, BIOCARTA, and HALLMARK databases downloaded from the Molecular Signature Database (https://www.gsea-msigdb.org/gsea/msigdb/) using the msigdb_gsets function.	KEGG suggested: (KEGG, RRID:SCR_012773)
   We finally calculated the Dissimilarity Index, for each pair of pseudotime related fitted gene expression (https://link.springer.com/content/pdf/10.1007/s11634-006-0004-6.pdf) using the TSclust package.	TSclust suggested: None
   For the heatmap comparing pathways activity in the four clusters, we used PROGENY (v 1.12.0) or the score described above with gene sets from the REACTOME database or the proliferation index and the normalized gene expression from the Seurat object as input.	PROGENY suggested: (PROGENY, RRID:SCR_006647) REACTOME suggested: (Reactome, RRID:SCR_003485)
   The raw counts were first normalized with the TMM method from the EdgeR package and expressed as count per million.	EdgeR suggested: (edgeR, RRID:SCR_012802)
   Public snRNA-Seq dataset integrated: GEO datasets were downloaded from Gene Expression Omnibus (	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)

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   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).

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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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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.10.05.463150v1 on bioRxiv

   Oct 6, 2021