Activation of the SARS-CoV-2 Receptor Ace2 through JAK/STAT-Dependent Enhancers during Pregnancy
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SciScore for 10.1101/2020.05.11.089045: (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
Experimental Models: Cell Lines Sentences Resources RNA-seq data of human bronchial cell line (BEAS-2B) and airway basal cells from human donors treated with IFNα2, IFNγ, IL4 or IL17A were obtained from GSE148829. BEAS-2Bsuggested: NoneSoftware and Algorithms Sentences Resources ) (version 0.36) and Bowtie (Langmead et al., 2009) (version 1.1.2), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Bowtiesuggested: (Bowtie, RRID:SCR_005476)Picard, … SciScore for 10.1101/2020.05.11.089045: (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
Experimental Models: Cell Lines Sentences Resources RNA-seq data of human bronchial cell line (BEAS-2B) and airway basal cells from human donors treated with IFNα2, IFNγ, IL4 or IL17A were obtained from GSE148829. BEAS-2Bsuggested: NoneSoftware and Algorithms Sentences Resources ) (version 0.36) and Bowtie (Langmead et al., 2009) (version 1.1.2), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Bowtiesuggested: (Bowtie, RRID:SCR_005476)Picard, http://broadinstitute.github.io/picard/. 2016) was used to remove duplicates and subsequently, Homer (Heinz et al., 2010) Picardsuggested: (Picard, RRID:SCR_006525)R and the packages dplyr (https://CRAN.R-project.org/package=dplyr) and ggplot2 (Love et al., 2014) were used for visualization. ggplot2suggested: (ggplot2, RRID:SCR_014601)Sequence read numbers were calculated using Samtools (Masella et al., 2016) software with sorted bam files. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)The correlation between the ChIP-seq replicates was computed using deepTools using Spearman correlation. deepToolssuggested: (Deeptools, RRID:SCR_016366)RNA-seq analysis: RNA-seq reads were analyzed using Trimmomatic (Bolger et al., 2014) Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)RNA-seq data shown in Fig. 1b and ChIP-seq data shown in Figure 2 were generated in our lab and deposited in the Gene Expression Omnibus (GEO) and ENCODE. ChIP-seqsuggested: (ChIP-seq, RRID:SCR_001237)Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)ENCODEsuggested: (Encode, RRID:SCR_015482)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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