Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs
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SciScore for 10.1101/2020.10.29.360800: (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 Specifically, peptides derived from the HIV-1 envelope were presumed not to truly bind with SARS-CoV-2 antibodies, so we used these HIV-1 peptides to estimate the FPR for a threshold under consideration: the number of HIV-1 sample-peptide pairs above this threshold divided by the total number of HIV-1 sample-peptide pairs in the library batch after the curation step. SARS-CoV-2suggested: NoneSoftware and Algorithms Sentences Resources Bacterial codon-optimized oligonucleotide libraries were designed using the Python script available at https://github.com/jbloomlab/phipseq_oligodesign. Pythonsuggested: …SciScore for 10.1101/2020.10.29.360800: (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 Specifically, peptides derived from the HIV-1 envelope were presumed not to truly bind with SARS-CoV-2 antibodies, so we used these HIV-1 peptides to estimate the FPR for a threshold under consideration: the number of HIV-1 sample-peptide pairs above this threshold divided by the total number of HIV-1 sample-peptide pairs in the library batch after the curation step. SARS-CoV-2suggested: NoneSoftware and Algorithms Sentences Resources Bacterial codon-optimized oligonucleotide libraries were designed using the Python script available at https://github.com/jbloomlab/phipseq_oligodesign. Pythonsuggested: (IPython, RRID:SCR_001658)We used the scipy.optimize package (Virtanen et al., 2020) to infer maximum likelihood estimates that would generate a set of mean normalized counts values across samples for each peptide, i. scipysuggested: (SciPy, RRID:SCR_008058)We used the pairwise2 function of the Biopython software package to perform the alignment (Cock et al.). Biopythonsuggested: (Biopython, RRID:SCR_007173)Results from OddPub: Thank you for sharing your code.
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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