Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells
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SciScore for 10.1101/2020.08.19.255901: (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
Antibodies Sentences Resources Flow cytometry: Following differentiation and protein pulse, MDDCs were washed and stained with antibodies specific for HLA-DR (L243, Biolegend), HLA-DRsuggested: NoneProduction and purification of HLA-specific antibodies: Hybridoma cells (clones W6/32, L243, B721) were cultured in a CELLine CL 1000 Bioreactor (Integra) as described in (31). B721suggested: (LSBio (LifeSpan Cat# LS-B721, RRID:AB_2190003)Antibody-resin complexes were then collected by gravity flow through chromatography columns, washed with 20 ml of PBS, and eluted with 5 ml 100 mM glycine pH 3.0. Antibody-resinsuggested: NoneLysate … SciScore for 10.1101/2020.08.19.255901: (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
Antibodies Sentences Resources Flow cytometry: Following differentiation and protein pulse, MDDCs were washed and stained with antibodies specific for HLA-DR (L243, Biolegend), HLA-DRsuggested: NoneProduction and purification of HLA-specific antibodies: Hybridoma cells (clones W6/32, L243, B721) were cultured in a CELLine CL 1000 Bioreactor (Integra) as described in (31). B721suggested: (LSBio (LifeSpan Cat# LS-B721, RRID:AB_2190003)Antibody-resin complexes were then collected by gravity flow through chromatography columns, washed with 20 ml of PBS, and eluted with 5 ml 100 mM glycine pH 3.0. Antibody-resinsuggested: NoneLysate clarification was achieved by centrifugation at 3,000 x g for 10 mins followed by a 20,000 × g spin step for 15 mins at 4°C. 3 mg of W6/32 antibody-PAS was incubated with lysate for at least 5 h at 4°C with gentle rotation. antibody-PASsuggested: NoneAntibody-resin-HLA complexes were washed with 15 ml of 0.005% IGEPAL, 50 mM Tris pH 8.0, 150 mM NaCl, 5 mM EDTA, 15 ml of 50 mM Tris pH 8.0, 150 mM NaCl, 15 ml of 50 mM Tris pH 8.0, 450 mM NaCl, and 15 ml of 50 mM Tris pH 8.0. Antibody-resin-HLAsuggested: NoneSoftware and Algorithms Sentences Resources Staining data were acquired on a LSRFortessa and analysis was performed on Flowjo software version 10.6.2. Flowjosuggested: (FlowJo, RRID:SCR_008520)NetMHCII pan 4.023 (http://www.cbs.dtu.dk/services/) was installed locally and utilised to define binding (rank score cut of 10). http://www.cbs.dtu.dk/services/suggested: (CBS Prediction Servers, RRID:SCR_002874)Jalview 2.11.1.0 63 was used for multisequence alignment with MAFFT (Multiple Alignment using Fast Fourier Transform) with default settings. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Alignments were visualised in Jalview and colouring amino acids by property based on CLustal_X definitions or identity. Jalviewsuggested: (Jalview, RRID:SCR_006459)All graphs were plotted in R or Excel. R or Excelsuggested: NoneResults 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.
- 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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