Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option

Article activity feed

1. Version published to 10.1038/s41588-020-00732-8

   Oct 19, 2020
2. 

   ScreenIT

   Jul 25, 2020

   SciScore for 10.1101/2020.07.24.219139: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   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
   Membranes were incubated with primary antibodies to ACE2 (1:1000; Abcam), FLAG (1:1000, clone M2; Sigma-Aldrich), HRP-conjugated secondary antibodies to rabbit and mouse (1:1000; Cell Signaling Technology), and HRP-conjugated actin (1:25000; Abcam).	ACE2 suggested: None FLAG suggested: (Advanced Targeting Systems Cat# AB-450-1000, RRID:AB_10584603) HRP-conjugated actin suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell stimulation: For …

   SciScore for 10.1101/2020.07.24.219139: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   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
   Membranes were incubated with primary antibodies to ACE2 (1:1000; Abcam), FLAG (1:1000, clone M2; Sigma-Aldrich), HRP-conjugated secondary antibodies to rabbit and mouse (1:1000; Cell Signaling Technology), and HRP-conjugated actin (1:25000; Abcam).	ACE2 suggested: None FLAG suggested: (Advanced Targeting Systems Cat# AB-450-1000, RRID:AB_10584603) HRP-conjugated actin suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell stimulation: For interferon stimulation experiments, 2 × 105 SCC-4 and SCC-25 cells were stimulated with 100 ng/mL IFN-α or IFN-γ (Abcam) or PBS for 48 hrs.	SCC-25 suggested: None
   Software and Algorithms
   Sentences	Resources
   RNAseq data from TCGA, GTEx, CCLE, and other studies were aligned to the cancer-tissue transcriptome assembly using GNU parallel (Tange, 2011) and Salmon v0.12.0 (Patro et al., 2017).	Salmon suggested: (Salmon, RRID:SCR_017036)
   We used the MUSCLE aligner on default settings to build a global alignment of human to rhesus macaque and marmoset, and then aligned all other species to the profile, reverting the strand of the whole sequence for mouse, elephant, cow and opossum due to whole gene inversions.	MUSCLE suggested: (MUSCLE, RRID:SCR_011812)
   Reads were adapter trimmed and filtered for minimal 35nt sequences using Trimmomatic.	Trimmomatic suggested: (Trimmomatic, RRID:SCR_011848)
   All reads were then mapped with HISAT2 (optional parameters −p 8 −q −k 5) against GRCh38 reference chromosome assembly.	HISAT2 suggested: (HISAT2, RRID:SCR_015530)
   The HISAT2 index here was built with the --exon / --ss option to cover all known splice sites annotated in the GENCODE v34 basic annotation.	GENCODE suggested: (GENCODE, RRID:SCR_014966)
   Flow Cytometry: For GFP detection, single-cell suspensions were run on a LSR Fortessa (BD Biosciences) running BD FACSDiva v8.0 and analysed with FlowJo v10 (Tree Star Inc.	BD FACSDiva suggested: (BD FACSDiva Software, RRID:SCR_001456) FlowJo suggested: (FlowJo, RRID:SCR_008520)

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.07.24.219139v1 on bioRxiv

   Jul 24, 2020