Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

Article activity feed

1. Version published to 10.1038/s41586-020-03148-w

   Jan 11, 2021
2. 

   ScreenIT

   Aug 6, 2020

   SciScore for 10.1101/2020.08.05.238188: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Human subjects: All human subjects research was approved by the Northwestern University Institutional Review Board. Consent: All subjects or their surrogates provided informed consent.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   FASTQ files were generated using bcl2fastq (Illumina).	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   0.6.4 and aligned to the hybrid genome described above using STAR 2.6.1d [47]	STAR suggested: (STAR, RRID:SCR_015899)
   Gene-level assignment was then performed using featureCounts 1.6.4 [48]	featureCounts suggest…

   SciScore for 10.1101/2020.08.05.238188: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Human subjects: All human subjects research was approved by the Northwestern University Institutional Review Board. Consent: All subjects or their surrogates provided informed consent.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   FASTQ files were generated using bcl2fastq (Illumina).	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   0.6.4 and aligned to the hybrid genome described above using STAR 2.6.1d [47]	STAR suggested: (STAR, RRID:SCR_015899)
   Gene-level assignment was then performed using featureCounts 1.6.4 [48]	featureCounts suggested: (featureCounts, RRID:SCR_012919)
   Data was processed using Scanpy v1.5.1 [52], doublets were detected with scrublet v0.2.1 [53] and removed, ribosomal genes were removed and multisample integration was performed with BBKNN v1.3.12 [54]	BBKNN suggested: None
   Computations were automated with snakemake v5.5.4 [56].	snakemake suggested: (Snakemake, RRID:SCR_003475)
   Deconvolution of bulk RNA-seq alveolar macrophage signatures was performed using AutoGeneS v1.0.3[57] and signatures derived from integrated single cell RNA-Seq object.	AutoGeneS suggested: None
   Visualization: All plotting was performed using ggplot2 version 3.3.1, with the exception of heatmaps, which were generated using pheatmap version 1.0.12.	ggplot2 suggested: (ggplot2, RRID:SCR_014601) pheatmap suggested: (pheatmap, RRID:SCR_016418)
   Figure layouts were generated using patchwork version 1.01 and edited in Adobe Illustrator 2020.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)

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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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3. 

   Version published to 10.1101/2020.08.05.238188 on bioRxiv

   Aug 5, 2020