Self-assembling short immunostimulatory duplex RNAs with broad-spectrum antiviral activity

Article activity feed

1. Version published to 10.1016/j.omtn.2022.08.031

   Sep 1, 2022
2. 

   ScreenIT

   Nov 30, 2021

   SciScore for 10.1101/2021.11.19.469183: (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	Contamination: All cell lines used in this study were free of mycoplasma, as confirmed by the LookOut Mycoplasma PCR Detection Kit (Sigma)

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibodies and Western blotting: The antibodies used in this study were anti-IRF3 (Abcam, ab68481), anti-IRF3	anti-IRF3 ( Abcam , ab68481) , suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   , MDA5 KO A549-DualTM cells (InvivoGen)	MDA5 KO suggested: None A549-DualTM suggested: None
   , TLR3 KO A549 cells (Abcam), HEK-BlueTM Null-k cells (InvivoGen, …

   SciScore for 10.1101/2021.11.19.469183: (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	Contamination: All cell lines used in this study were free of mycoplasma, as confirmed by the LookOut Mycoplasma PCR Detection Kit (Sigma)

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibodies and Western blotting: The antibodies used in this study were anti-IRF3 (Abcam, ab68481), anti-IRF3	anti-IRF3 ( Abcam , ab68481) , suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   , MDA5 KO A549-DualTM cells (InvivoGen)	MDA5 KO suggested: None A549-DualTM suggested: None
   , TLR3 KO A549 cells (Abcam), HEK-BlueTM Null-k cells (InvivoGen, hkb-null1k), HEK-BlueTM hTLR7 cells (InvivoGen, htlr7), THP1-DualTM cells (InvivoGen, thpd-nifs), THP1-DualTM KO-TLR8 cells (InvivoGen,kotlr8)	THP1-DualTM suggested: None KO-TLR8 suggested: RRID:CVCL_A8BW)
   , MDCK cells (ATCC CRL-2936), and LLC-MK2 cells (ATCC CCL-7.1) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Life Technologies) and penicillin-streptomycin (Life Technologies).	LLC-MK2 suggested: None
   HCoV-NL63 was obtained from the ATCC and expanded in LLC-MK2 cells.	HCoV-NL63 suggested: RRID:CVCL_RW88)
   Both influenza virus strains were expanded in MDCK cells.	MDCK suggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)
   Native SARS-CoV-2 infection and inhibition by RNA treatment: ACE2-expressing A549 cells (a gift from Brad Rosenberg) were transfected with indicated RNAs.	A549 suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
   24 h post-transfection, the transfected ACE2-A549 cells were infected with SARS-CoV-2 (MOI = 0.05) for 48 hours.	ACE2-A549 suggested: None
   Native SARS-CoV-1 and MERS-CoV infection and inhibition by RNA treatment: Vero E6 cells (ATCC# CRL 1586) were cultured in DMEM (Quality Biological), supplemented with 10% (v/v)	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   RNA-seq and Gene ontogeny analysis: RNA-seq was processed by Genewiz using a standard RNA-seq package that includes polyA selection and sequencing on an Illumina HiSeq with 150-bp pair-ended reads.	Genewiz suggested: (GENEWIZ, RRID:SCR_003177)
   Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.	Trimmomatic suggested: (Trimmomatic, RRID:SCR_011848)
   The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.	STAR suggested: (STAR, RRID:SCR_004463)
   Unique gene hit counts were calculated by using feature Counts from the Subread package v.	Subread suggested: (Subread, RRID:SCR_009803)
   1.5.2 followed by differential expression analysis using DESeq2.	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   Gene Ontology analysis was performed using DAVID (46).	DAVID suggested: (DAVID, RRID:SCR_001881)
   Volcano plots and heat maps were generated using the EnhancedVolcano R package (47).	EnhancedVolcano suggested: (EnhancedVolcano, RRID:SCR_018931)
   Database searching included all entries from the Human UniProt database (downloaded: 2014-02-04) This database was concatenated with one composed of all protein sequences in the reversed order.	Human UniProt suggested: None
   Raw data were submitted to ProteomeXchange via the PRIDE database with the accession PXD027838. qRT-PCR: Total RNA was extracted from cells using RNeasy Plus Mini Kit (QiaGen, Cat#74134) according to the manufacturer’s instructions.	PRIDE suggested: (Pride-asap, RRID:SCR_012052)
   Fluorescence imaging was carried out using a confocal laser-scanning microscope (SP5 X MP DMI-6000, Germany) and image processing was done using Imaris software (Bitplane, Switzerland)	Imaris suggested: (Imaris, RRID:SCR_007370)
   Native SARS-CoV-1 and MERS-CoV infection and inhibition by RNA treatment: Vero E6 cells (ATCC# CRL 1586) were cultured in DMEM (Quality Biological), supplemented with 10% (v/v)	Quality Biological suggested: None

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   Results from OddPub: Thank you for sharing your data.

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

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3. 

   Version published to 10.1101/2021.11.19.469183 on bioRxiv

   Nov 22, 2021