Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2

Article activity feed

1. Version published to 10.1016/j.stem.2020.10.004

   Dec 1, 2020
2. 

   ScreenIT

   Jul 11, 2020

   SciScore for 10.1101/2020.07.10.194498: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   Consent: Appropriate Human Tissue Act (HTA) guidance was followed; For organoids used for viral infection and following analysis, human lung tissue was obtained from patients undergoing lobectomy surgery at Seoul National University Hospital (SNUH) with written informed consent from approval of the ethical committee (approval no. C-1809-137-975). IRB: Appropriate Human Tissue Act (HTA) guidance was followed; For organoids used for viral infection and following analysis, human lung tissue was obtained from patients undergoing lobectomy surgery at Seoul National University Hospital (SNUH) with written informed consent from approval of the ethical committee …

   SciScore for 10.1101/2020.07.10.194498: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Appropriate Human Tissue Act (HTA) guidance was followed; For organoids used for viral infection and following analysis, human lung tissue was obtained from patients undergoing lobectomy surgery at Seoul National University Hospital (SNUH) with written informed consent from approval of the ethical committee (approval no. C-1809-137-975). IRB: Appropriate Human Tissue Act (HTA) guidance was followed; For organoids used for viral infection and following analysis, human lung tissue was obtained from patients undergoing lobectomy surgery at Seoul National University Hospital (SNUH) with written informed consent from approval of the ethical committee (approval no. C-1809-137-975).
   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
   Cells were prepared for flow cytometry with primary antibodies CD31-APC (Biolegend, 303116), CD45-APC (Biolegend, 368512), EpCAM-FITC (Biolegend, 324204) and HTII-280-IgM (Terrace Biotech, TB-27AHT2-280) at 1:40 per 4 million cells for 30 min on ice.	CD45-APC suggested: None EpCAM-FITC suggested: None
   Following permeabilisation, organoid sections were blocked for 1 hr in 5% normal donkey serum in PBS at RT, and incubated with primary antibody mixes overnight at 4 °C at the following dilutions; rabbit pro-SFTPC (1:500, Millipore, Ab3786), mouse anti-HTII-280 (1:500	pro-SFTPC suggested: None anti-HTII-280 suggested: None
   Antibodies were E-cadherin (R&D, AF748, 1:300), NP (Sino, 40143-MM05, 1:200)	E-cadherin suggested: (R and D Systems Cat# AF748, RRID:AB_355568) AF748 suggested: (R and D Systems Cat# AF748, RRID:AB_355568)
   Experimental Models: Cell Lines
   Sentences	Resources
   HTII-280− cells were cultured as with HTII-280+, although with a few minor differences.	HTII-280− suggested: None
   After infection, remove infection media and wash the Vero cells with PBS two times, mixed agar and Modified Eagle’s Medium (Thermofisher) were poured on each well.	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   Software and Algorithms
   Sentences	Resources
   Cell sorting was performed on an Aria III fusion (BD Biosciences) using a 100 μM nozzle, and data were analysed with FlowJo software (Tree Star, Inc.).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Single-cell RNA sequencing and data processing: Fastq file was aligned and each UMI count was calculated using Cell Ranger software provided by the manufacturer (10X Genomics).	Cell Ranger suggested: (Cell Ranger , RRID:SCR_017344)

   ---

   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 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).

   ---

   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32 and 26. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.07.10.194498v1 on bioRxiv

   Jul 10, 2020