Nonstructural protein 1 widespread RNA decay phenotype varies among coronaviruses

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1. Version published to 10.1016/j.isci.2022.105887

   Jan 1, 2023
2. 

   ScreenIT

   Apr 22, 2022

   SciScore for 10.1101/2022.04.19.488803: (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
   20ug of each sample were resolved by SDS-PAGE and Western blotted with following antibodies in TBST (Tris-buffered saline, 0.1% Tween 20): mouse anti-Flag at 1:1000 (Invitrogen) and rabbit anti-Vinculin at 1:2000 (Invitrogen).	anti-Flag suggested: (Advanced Targeting Systems Cat# AB-450-1000, RRID:AB_10584603) anti-Vinculin suggested: None
   Primary antibody incubations were followed by horseradish peroxidase (HRP)-conjugated goat anti-mouse or goat anti-rabbit secondary antibodies (1:5000; …

   SciScore for 10.1101/2022.04.19.488803: (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
   20ug of each sample were resolved by SDS-PAGE and Western blotted with following antibodies in TBST (Tris-buffered saline, 0.1% Tween 20): mouse anti-Flag at 1:1000 (Invitrogen) and rabbit anti-Vinculin at 1:2000 (Invitrogen).	anti-Flag suggested: (Advanced Targeting Systems Cat# AB-450-1000, RRID:AB_10584603) anti-Vinculin suggested: None
   Primary antibody incubations were followed by horseradish peroxidase (HRP)-conjugated goat anti-mouse or goat anti-rabbit secondary antibodies (1:5000; Southern Biotechnology) RT-qPCR: Total RNA was harvested using TRIzol according to the manufacture’s protocol.	anti-mouse suggested: None anti-rabbit suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells, Transfections, and Lentiviral Transduction: HEK293T cells (ATCC) were grown in Dulbecco’s modified Eagle’s medium (DMEM-Invitrogen) supplemented with 10% fetal bovine serum (FBS).	HEK293T suggested: None
   Recombinant DNA
   Sentences	Resources
   Plasmids and Plasmid Construction: The pLVX-TetOne-Zeo-SARS2-NSP1-3xFlag and pLVX-TetOne-Zeo-MERS-NSP1-3xFlag, pcDNA4 CoV2 nsp1 m1 3xFlag and pcDNA MERS nsp1 m1 3xFlag were a kind gift from the Glaunsinger Lab.	pLVX-TetOne-Zeo-SARS2-NSP1-3xFlag suggested: None pLVX-TetOne-Zeo-MERS-NSP1-3xFlag suggested: None pcDNA4 suggested: RRID:Addgene_45906)
   To establish the lentiviral cell lines, HEK293T cells were co-transfected with their respective zeocine-resistant, lentiviral vector along with pMD2.G and psPAX2 the envelop, packaging, and accessory plasmids in DMEM 0% FBS with using Polyjet (SignaGen).	pMD2.G suggested: RRID:Addgene_12259) psPAX2 suggested: RRID:Addgene_12260)
   Software and Algorithms
   Sentences	Resources
   For DNA transfection, HEK293T cells were plated and transfected after 24h when 70% confluent using PolyJet (SignaGen).	PolyJet suggested: None
   Using Galaxy[41] reads were then aligned to the human genome (hg38) by Bowtie2 and differential expression analysis were performed using Cufflink and Cuffdiff[42].	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368) Cufflink suggested: (Cufflinks, RRID:SCR_014597)
   Hierarchical clustering was generated in Python using the SciPy package with complete linkage and Euclidian distance.	Python suggested: None SciPy suggested: None
   Raw data was filtered based on the number of peptides for each hit and Gene Ontology (GO) enrichment analysis was performed on the human interacting proteins for each coronavirus using DAVID bioinformatic database.	DAVID suggested: None
   Top enriched and shared clusters are identified on the network using the Cytoscape software Statistical analysis: All results are expressed as means ± standard errors of the means (SEMs) of experiments independently repeated at least three times (individual replicate points are shown on bar graphs).	Cytoscape suggested: None

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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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
3. 

   Version published to 10.1101/2022.04.19.488803v1 on bioRxiv

   Apr 19, 2022