Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms

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1. Version published to 10.1016/j.xcrm.2021.100288

   May 1, 2021
2. 

   ScreenIT

   Sep 16, 2020

   SciScore for 10.1101/2020.09.11.293464: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All procedures used in this study (sex-matched, age-matched) complied with federal guidelines and the institutional policies of the Yale School of Medicine Animal Care and Use Committee.
   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

   Antibodies
   Sentences	Resources
   Plates were washed three times with PBS-T (PBS with 0.1% Tween-20) and 50μl of mouse IgG-specific secondary antibody (BioLegend #405306, 1:10,000) diluted in dilution solution added to each well.	mouse IgG-specific suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Gen…

   SciScore for 10.1101/2020.09.11.293464: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All procedures used in this study (sex-matched, age-matched) complied with federal guidelines and the institutional policies of the Yale School of Medicine Animal Care and Use Committee.
   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

   Antibodies
   Sentences	Resources
   Plates were washed three times with PBS-T (PBS with 0.1% Tween-20) and 50μl of mouse IgG-specific secondary antibody (BioLegend #405306, 1:10,000) diluted in dilution solution added to each well.	mouse IgG-specific suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Generation of SARS-CoV-2 virus: To generate SARS-CoV-2 viral stocks, Huh7.5 cells were inoculated with SARS-CoV-2 isolate USA-WA1/2020 (BEI Resources #NR-52281) to generate a P1 stock.	Huh7.5 suggested: RRID:CVCL_7927)
   Virus titer was determined by plaque assay using Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Cytokine assays: Soluble chemokines and cytokines were assessed in CSF supernatant and paired plasma using the HD71 Human Cytokine Array/Chemokine Array (Eve Technologies, Calgary, AB).	AB suggested: RRID:BDSC_203)
   Software and Algorithms
   Sentences	Resources
   To identify potential intercellular interactions between different cell types in the scRNA-seq data, we utilized CellPhoneDB v2(10)	CellPhoneDB suggested: (CellPhoneDB, RRID:SCR_017054)
   Assignments of V(D)J sequences were performed using IgBLAST v.	IgBLAST suggested: (IgBLAST, RRID:SCR_002873)
   Statistical methods: All statistical analyses were performed using commercially available software (Prism or Excel).	Prism or Excel suggested: None
   Human Monoclonal antibodies: Data availability: Gene expression and repertoire data in the study are available in the NCBI repository SRAxxxx Raw mass spectrometry files and data analysis output are available from MassIVE (https://massive.ucsd.edu/) and Proteome Exchange (http://www.proteomexchange.org/) under MassIVE dataset identifier # and Proteome Exchange # Competing Interests: None of the authors declare interests related to the manuscript.	MassIVE suggested: None http://www.proteomexchange.org/ suggested: (ProteomeXchange, RRID:SCR_004055)

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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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3. 

   Version published to 10.1101/2020.09.11.293464 on bioRxiv

   Sep 12, 2020