Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
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SciScore for 10.1101/2020.06.08.20122143: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Human Subjects: For in vitro studies on human PBMCs and monocytes, buffy coats from healthy donors were obtained from Sanquin blood bank, Nijmegen after written informed consent.
IRB: The study was approved by the local medical ethics committee of the Radboudumc under reference number: 2020–6359.Randomization For unsupervised computation analysis, FCS files were randomly down sampled to 20,000 events of the pre-processed files and subsequently concatenated to a single file containing all events. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Antibodies and dilutions … SciScore for 10.1101/2020.06.08.20122143: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Human Subjects: For in vitro studies on human PBMCs and monocytes, buffy coats from healthy donors were obtained from Sanquin blood bank, Nijmegen after written informed consent.
IRB: The study was approved by the local medical ethics committee of the Radboudumc under reference number: 2020–6359.Randomization For unsupervised computation analysis, FCS files were randomly down sampled to 20,000 events of the pre-processed files and subsequently concatenated to a single file containing all events. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Antibodies and dilutions used are CD45-BV510 (Biolegend, 1:100), CD14-PC7 (eBioscience, 1:100), CD16-FITC (eBioscience, 1:100), CD3-APC750 (Beckman Coulter, 1:50), CD19-APC-R700 (Becton Dickinson, 1:100), CD56-APC (Beckman Coulter, 1:50), HLADR-PE (Beckman Coulter, 1:20), CD11b-BV785 (Biolegend, 1:100), CCR2-BV421 (Becton Dickinson, 1:50), CX3CR1-BV650 (Biolegend, 1:50) and Live/Dead FVS620 (Becton Dickinson, according to manufacturers’ instructions). CD14-PC7suggested: (Beckman Coulter Cat# A22331, RRID:AB_10639528)CD16-FITCsuggested: NoneCD11b-BV785suggested: NoneCX3CR1-BV650suggested: NoneIn short, 500,000 cells were incubated overnight with 1 μg H3K4me3 or H3K27Ac antibody (Diagenode) and protein A magnetic beads at 4 °C. H3K4me3suggested: NoneH3K27Acsuggested: NoneSoftware and Algorithms Sentences Resources Unsupervised clustering was performed on the expression values of all markers using the tSNE plugin in FlowJo (Becton Dickinson, version 10.6.2), using 1000 iterations and a perplexity of 30. FlowJosuggested: (FlowJo, RRID:SCR_008520)Library preparation and sequencing of ChIP samples: ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. ChIP-seqsuggested: (ChIP-seq, RRID:SCR_001237)Data was analyzed using GraphPad Prism 5.0. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)RNA-seq data analysis: RNA-sequencing reads were aligned with Hisat2 version 2.0.4 to the provided and pre-indexed hg38 transcript assembly from UCSC, with alignment tailoring for transcript assemblers enabled44. Hisat2suggested: (HISAT2, RRID:SCR_015530)Samtools was used to filter reads with a quality score lower than 20, and PCR duplicates were removed with Picard45. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)The ‘rlogTransformation’ function in DESeq2 was used to normalize, transform and noise-stabilize the expression data for visualization purposes. DESeq2suggested: (DESeq, RRID:SCR_000154)A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in each sample53. BEDToolssuggested: (BEDTools, RRID:SCR_006646)Figures were generated in R with the ggplot2 and ComplexHeatmap R packages47–49. ggplot2suggested: (ggplot2, RRID:SCR_014601)ComplexHeatmapsuggested: (ComplexHeatmap, RRID:SCR_017270)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).
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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