Impaired activation of transposable elements in SARS‐CoV‐2 infection
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SciScore for 10.1101/2021.02.25.432821: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Datasets: The original sequencing datasets for IAV infection in A549 cells and the Blanco-Melo et al datasets can be found on the NCBI Gene Expression Omnibus (GEO) server under the accession numbers GSE133329 and GSE147507, respectively. A549suggested: NoneSoftware and Algorithms Sentences Resources Datasets: The original sequencing datasets for IAV infection in A549 cells and the Blanco-Melo et al datasets can be found on the NCBI Gene Expression Omnibus (GEO) server under the accession numbers GSE133329 and GSE147507, respectively. Gene Expression Omnibussuggested: (Gene Expression …SciScore for 10.1101/2021.02.25.432821: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Datasets: The original sequencing datasets for IAV infection in A549 cells and the Blanco-Melo et al datasets can be found on the NCBI Gene Expression Omnibus (GEO) server under the accession numbers GSE133329 and GSE147507, respectively. A549suggested: NoneSoftware and Algorithms Sentences Resources Datasets: The original sequencing datasets for IAV infection in A549 cells and the Blanco-Melo et al datasets can be found on the NCBI Gene Expression Omnibus (GEO) server under the accession numbers GSE133329 and GSE147507, respectively. Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012), 2020): Preprocessing and alignment: Raw reads from GSE147507 and GSE133329 were trimmed to remove Illumina adapters using the Trimmomatic software (Bolger et al., 2014) version 0.39. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)We used the STAR aligner version 2.7.1a (Dobin et al., 2013) to align raw reads to human RefSeq reference genome (GRCh38). RefSeqsuggested: (RefSeq, RRID:SCR_003496)For ChIP-Seq data, alignment with STAR was followed by filtering out of non-uniquely mapped reads. STARsuggested: (STAR, RRID:SCR_015899)This was followed by differential expression analysis using DESeq2 (Love et al., 2014). DESeq2suggested: (DESeq, RRID:SCR_000154)To quantify gene expression and to determine the locations of individual TEs that change in expression we used featureCounts v2.0.0 (Jin et al., 2015; Liao et al., 2014) from the Subread package which uses only uniquely mapped reads. featureCountssuggested: (featureCounts, RRID:SCR_012919)Subreadsuggested: (Subread, RRID:SCR_009803)The list of epifactors was downloaded from https://epifactors.autosome.ru/ (Medvedeva et al., 2015) https://epifactors.autosome.ru/suggested: (EpiFactors , RRID:SCR_016956)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.
- No funding statement was detected.
- No protocol registration statement was detected.
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