Mutating novel interaction sites in NRP1 reduces SARS-CoV-2 spike protein internalization
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SciScore for 10.1101/2021.10.11.463689: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources HA antibody (HA.C5 #18181; 1:1000) and LAMP1 antibody (#24170) were purchased from Abcam. LAMP1suggested: (Abcam Cat# ab24170, RRID:AB_775978)M2 anti Flag Mouse antibody (#SLBT7654; 1:5000) and Actin (#087M4850; 1:10,000) were purchased from Sigma. M2 anti Flag Mouse antibody (#SLBT7654; 1:5000)suggested: Noneanti Flag Mouse antibodysuggested: NoneActinsuggested: NoneExperimental Models: Cell Lines Sentences Resources Mammalian cell culture, transfection, and drug treatment: HeLa and HEK … SciScore for 10.1101/2021.10.11.463689: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources HA antibody (HA.C5 #18181; 1:1000) and LAMP1 antibody (#24170) were purchased from Abcam. LAMP1suggested: (Abcam Cat# ab24170, RRID:AB_775978)M2 anti Flag Mouse antibody (#SLBT7654; 1:5000) and Actin (#087M4850; 1:10,000) were purchased from Sigma. M2 anti Flag Mouse antibody (#SLBT7654; 1:5000)suggested: Noneanti Flag Mouse antibodysuggested: NoneActinsuggested: NoneExperimental Models: Cell Lines Sentences Resources Mammalian cell culture, transfection, and drug treatment: HeLa and HEK 293T cells were obtained from ATCC and maintained in a humidified atmosphere at 5% CO2 in Dulbecco’s Modified Eagle’s (DMEM) complete medium (Corning) supplemented with 10% fetal bovine serum (FBS; Seradigm) in 37°C. HeLasuggested: NoneWestern Blotting and immunoprecipitation: For immunoprecipitation, either HA-tagged NRP1 (or mutants) and Flag-tagged SARS-CoV-2-S (or S1493-685) mutant or HA-tagged NRP1 (or mutants) and Flag-Plexin-A1 were expressed where indicated in 293T cells for 30 hours. 293Tsuggested: NoneRNA-seq analysis: For RNA-seq analysis, Total RNA was extracted from HEK293T cell line 30 hours post transfection (HA-NRP1 and SARS-CoV-2-S1493-685 and or HA-NRP1-4Cys-4Ala and SARS-CoV-2-S1493-685) using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. HEK293Tsuggested: NoneRecombinant DNA Sentences Resources Plasmids and recombinant proteins: HA-NRP1 and different mutants of HA-NRP1, Flag-Plexin-A1, Flag-SARS-CoV-2-S-original (NC_045512.2), Flag-SARS-CoV-2-B.1.1.7-S, Flag-SARS-CoV-B.1.351-S were all obtained from GenScript (Cloned into pcDNA 3.1 vector). pcDNA 3.1suggested: RRID:Addgene_20407)For cycloheximide stability assay, 293T cells were transfected with the constructs encoding HA-NRP1 or HA-NRP1 mutants. HA-NRP1suggested: NoneSoftware and Algorithms Sentences Resources The PAN domain coordinates from Uniprot were used to extract the PAN domain sequences from the full-length proteins which were then aligned with MAFFT linsi(54). MAFFTsuggested: (MAFFT, RRID:SCR_011811)The alignment was visualized with Geneious. Geneioussuggested: (Geneious, RRID:SCR_010519)The raw RNA-seq reads have been deposited at NCBI under BioProject ID PRJNA767890. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Reads were mapped with bowtie2 v2.2.5. (55). bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Differential expression analysis was performed with DESeq2, genes with an adjusted p-value less than 0.05 were considered differentially expressed (56). DESeq2suggested: (DESeq, RRID:SCR_000154)Statistical analysis: Statistical analyses were performed on individual experiments, as indicated, with GraphPad Prism 8 Software using an unpaired t-Test, equal variance for comparison between two groups and one-way ANOVA for comparisons between more than two groups. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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 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.
Results from scite Reference Check: We found no unreliable references.
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