Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro

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1. Version published to 10.1126/scitranslmed.abe9599

   Jun 16, 2021
2. 

   ScreenIT

   Sep 9, 2020

   SciScore for 10.1101/2020.09.02.280180: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: This study was approved by the Partners Healthcare Institutional Review Board under protocol 2017P001681.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The permeabilized cells were then stained with a pSTAT3-Y705 antibody (clone 13A3-1, BioLegend) for 30 mins on ice.	pSTAT3-Y705 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HUVEC and HRE co-culture and flow sorting: Primary HUVECs and HREs were purchased from Lonza and cultured in EGM-2 and REGM, respectively.	HUVEC suggested: KCB Cat# KCB …

   SciScore for 10.1101/2020.09.02.280180: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: This study was approved by the Partners Healthcare Institutional Review Board under protocol 2017P001681.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The permeabilized cells were then stained with a pSTAT3-Y705 antibody (clone 13A3-1, BioLegend) for 30 mins on ice.	pSTAT3-Y705 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HUVEC and HRE co-culture and flow sorting: Primary HUVECs and HREs were purchased from Lonza and cultured in EGM-2 and REGM, respectively.	HUVEC suggested: KCB Cat# KCB 200648YJ, RRID:CVCL_2959)
   To improve cell viability, HUVECs were cultured in tissue culture plates pre-coated with Matrigel (Corning) diluted 1:100 in EBM-2 (Lonza).	HUVECs suggested: None
   Software and Algorithms
   Sentences	Resources
   STAR was used to align sequencing reads to the UCSC hg19 transcriptome and RSEM was used to generate an expression matrix for all samples.	STAR suggested: (STAR, RRID:SCR_015899) RSEM suggested: (RSEM, RRID:SCR_013027)
   Both raw count and transcripts per million data were analyzed using edgeR and custom python scripts.	edgeR suggested: (edgeR, RRID:SCR_012802) python suggested: (IPython, RRID:SCR_001658)
   RNA velocity analysis was performed using the scVelo package60 using the default parameters.	scVelo suggested: (scVelo, RRID:SCR_018168)
   STAR was used to align sequencing reads to the UCSC hg19 transcriptome and RSEM was used to generate an expression matrix for all samples.	STAR suggested: (STAR, RRID:SCR_015899) RSEM suggested: (RSEM, RRID:SCR_013027)
   CRISPR-Cas9 editing of CD34+ HSPCs: Cas9 protein, pre-designed guide RNAs targeting IL6ST, IL6R, IL10RA, and IL10RB and non-targeting guide RNAs (from GeCKO v2 library) were purchased from Integrated DNA Technologies.	GeCKO suggested: (Gecko, RRID:SCR_009001)
   Flow cytometry data were acquired on a Cytoflex LX (Beckman Coulter) and analyzed using FlowJo v10.1.	FlowJo suggested: (FlowJo, RRID:SCR_008520)

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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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32 and 9. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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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   Read the original source
3. 

   Version published to 10.1101/2020.09.02.280180v1 on bioRxiv

   Sep 2, 2020