Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option
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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). ACE2suggested: NoneFLAGsuggested: (Advanced Targeting Systems Cat# AB-450-1000, RRID:AB_10584603)HRP-conjugated actinsuggested: NoneExperimental 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). ACE2suggested: NoneFLAGsuggested: (Advanced Targeting Systems Cat# AB-450-1000, RRID:AB_10584603)HRP-conjugated actinsuggested: NoneExperimental 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-25suggested: NoneSoftware 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). Salmonsuggested: (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. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)Reads were adapter trimmed and filtered for minimal 35nt sequences using Trimmomatic. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)All reads were then mapped with HISAT2 (optional parameters −p 8 −q −k 5) against GRCh38 reference chromosome assembly. HISAT2suggested: (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. GENCODEsuggested: (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 FACSDivasuggested: (BD FACSDiva Software, RRID:SCR_001456)FlowJosuggested: (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.
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