Host transcriptional response to SARS‐CoV‐2 infection in COVID‐19 patients
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SciScore for 10.1101/2021.05.13.443721: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Sample preparation and sequencing: This study was approved by the Institutional Ethics Committee to use patient samples for sequencing and all guidelines were followed. Sex as a biological variable There were 11 females and 30 males in our dataset. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Data Processing and Analysis: Raw sequencing reads were checked for quality using FASTQC v0.11.9 [41] and illumina universal adapters and low-quality reads were removed using cutadapt 2.8 [42]. FASTQCsuggested: (FastQC, RRID:SCR_014583)The processed reads were then again checked for quality using FASTQC and then … SciScore for 10.1101/2021.05.13.443721: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Sample preparation and sequencing: This study was approved by the Institutional Ethics Committee to use patient samples for sequencing and all guidelines were followed. Sex as a biological variable There were 11 females and 30 males in our dataset. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Data Processing and Analysis: Raw sequencing reads were checked for quality using FASTQC v0.11.9 [41] and illumina universal adapters and low-quality reads were removed using cutadapt 2.8 [42]. FASTQCsuggested: (FastQC, RRID:SCR_014583)The processed reads were then again checked for quality using FASTQC and then mapped to the human genome GRCh38 using STAR 2.7.3a with default parameters [43]. STARsuggested: (STAR, RRID:SCR_004463)The STAR index was generated using the GRCh38 genome and annotation gtf file downloaded from ENSEMBL [44]. ENSEMBLsuggested: (Ensembl, RRID:SCR_002344)BAM files generated were then sorted according to position using Samtools 1.10 [45]. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)The quality of BAM was assessed using QualiMap v. QualiMapsuggested: (QualiMap, RRID:SCR_001209)Uniquely aligned reads were counted using HTSeq [48]. HTSeqsuggested: (HTSeq, RRID:SCR_005514)Differential gene expression analysis was performed using DESeq2_1.24.0 [49]. DESeq2_1.24.0suggested: NoneFor PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package. DESeq2suggested: (DESeq, RRID:SCR_000154)KEGG) pathway analysis. KEGGsuggested: (KEGG, RRID:SCR_012773)Similar enriched terms were further merged using the ‘simplify’ function of clusterProfiler with similarity cutoff set to 0.7. ‘p.adjust’ was used as a feature to select representative terms and ‘min’ was used to select features. clusterProfilersuggested: (clusterProfiler, RRID:SCR_016884)Bedtools closest searches for overlapping features in two bed files. Bedtoolssuggested: (BEDTools, RRID:SCR_006646)Results from OddPub: Thank you for sharing your data.
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.
Results from scite Reference Check: We found no unreliable references.
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