The coding capacity of SARS-CoV-2

Version published to 10.1038/s41586-020-2739-1

Sep 9, 2020

SciScore for 10.1101/2020.05.07.082909: (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
Cells were washed and labeled with anti-rabbit FITC antibody and with DAPI (4=,6-diamidino-2-phenylindole).	anti-rabbit FITC suggested: None
Experimental Models: Cell Lines
Sentences	Resources
It was propagated (4 passages) and tittered on Vero E6 cells and then sequenced (details below) before in was used.	Vero E6 suggested: RRID:CVCL_XD71)
Cells were then placed on ice, washed twice with PBS containing 100μg/mL CHX, scraped from the T-75 flasks (Vero cells) or 10cm plates (Calu3 cells), pelleted and lysed with lysis buffer (1% triton in 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol supplemented …

SciScore for 10.1101/2020.05.07.082909: (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
Cells were washed and labeled with anti-rabbit FITC antibody and with DAPI (4=,6-diamidino-2-phenylindole).	anti-rabbit FITC suggested: None
Experimental Models: Cell Lines
Sentences	Resources
It was propagated (4 passages) and tittered on Vero E6 cells and then sequenced (details below) before in was used.	Vero E6 suggested: RRID:CVCL_XD71)
Cells were then placed on ice, washed twice with PBS containing 100μg/mL CHX, scraped from the T-75 flasks (Vero cells) or 10cm plates (Calu3 cells), pelleted and lysed with lysis buffer (1% triton in 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol supplemented with 10 U/ml Turbo DNase and 100μg/ml cycloheximide).	Calu3 suggested: RRID:CVCL_EQ19)
Briefly, linker (CTGTAGGCACCATCAAT) and poly-A sequences were removed and the remaining reads from were aligned to the Chlorocebus sabaeus genome (ENSEMBL release 99) and to the SARS-Cov-2 genomes [Genebank NC_045512.2 with 3 changes to match the used strain (BetaCoV/Germany/BavPat1/2020 EPI_ISL_406862), 241:C->T, 3037:C->T, 23403:A->G]. (infection of Vero cells) or to the Hg19 and NC_045512.2 with the same sequence changes (infection of Calu3).	Vero suggested: None
Software and Algorithms
Sentences	Resources
Novel junctions were mapped using STAR 2.5.3a aligner 40, with running flags as suggested at Kim et. al., to overcome filtering of non-canonical junctions.	STAR suggested: (STAR, RRID:SCR_015899)
For libraries of infected Vero cells sequencing reads were aligned using Bowtie to a fasta file containing chromosome 20 of Chlorocebus sabaeus (1240 annotated start codons, downloaded from ensembl: ftp://ftp.ensembl.org/pub/release99/fasta/chlorocebus_sabaeus/dna/) and the genomic sequence of SARS-CoV-2 (Refseq NC_045512.2).	Bowtie suggested: (Bowtie, RRID:SCR_005476)
For libraries of infected Calu3 cells sequencing reads were mapped to a fasta file containing chromosome 1 of hg19 (2843 annotated start codons) and the genomic sequence of SARS-CoV-2 (Refseq NC_045512.2).	Refseq suggested: (RefSeq, RRID:SCR_003496)
For the data that was generated from infected Vero cells at 5hpi training and ORF prediction by PRICE were done once using the CHX data from both replicates, and again using all Ribo-seq libraries from both replicates, and the resulting predictions were combined.	PRICE suggested: (PRICE, RRID:SCR_013063)
Data availability: All next-generation sequencing data files were deposited in Gene Expression Omnibus under accession number GSE149973.	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
All the RNA-seq and ribosome profiling data generated in this study can be accessed through a UCSC browser session: http://genome.ucsc.edu/s/aharonn/CoV2%2DTranslation	UCSC browser suggested: None

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.

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The coding capacity of SARS-CoV-2

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