Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-months recovery of COVID-19

Article activity feed

1. Version published to 10.3389/fcell.2022.1001558

   Oct 3, 2022
2. 

   ScreenIT

   Apr 25, 2022

   SciScore for 10.1101/2022.04.19.22274029: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethical approval for the study was obtained by the Ethics Committee for Clinical Research of Reproductive Medicine Center, Tongji Medical College, Huazhong University of Science and Technology. Consent: All participants included in the study gave informed consent.
   Sex as a biological variable	9 male patients at recovery stage and 5 male healthy controls were recruited for this study.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: SAMtools (v1.3.1) was used to sort bam files by genomic coordination and make a bam file index.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   To include as many non-uniquely mapped …

   SciScore for 10.1101/2022.04.19.22274029: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethical approval for the study was obtained by the Ethics Committee for Clinical Research of Reproductive Medicine Center, Tongji Medical College, Huazhong University of Science and Technology. Consent: All participants included in the study gave informed consent.
   Sex as a biological variable	9 male patients at recovery stage and 5 male healthy controls were recruited for this study.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: SAMtools (v1.3.1) was used to sort bam files by genomic coordination and make a bam file index.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   To include as many non-uniquely mapped reads as possible, trimmed reads were firstly aligned to human genome (hg19) by STAR (v2.7.5b) (Dobin et al., 2013) with default settings including parameters ‘-- winAnchorMultimapmax 2000 --outFilterMultimapNmax 1000’	STAR suggested: None
   UCSC genome browser was used for snapshots of transcriptome.	UCSC genome browser suggested: (UCSC Genome Browser, RRID:SCR_005780)
   R package Deseq2 (v1.28.1) (Love et al., 2014) was used to obtain differentially expressed genes (DEGs) and differentially expressed TEs (DETEs).	Deseq2 suggested: None
   Principal component analysis (PCA) was performed using DESeq2 normalized counts for DEGs/DETEs. Metascape (Zhou et al., 2019) was used to visualize functional profiles of genes and gene clusters.	Metascape suggested: (Metascape, RRID:SCR_016620)
   Images were organized by Adobe Illustrator.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)
   WGBS data processing and quality control: Raw reads were processed with Trim Galore (v0.6.4) to remove adaptor sequences and poor quality bases with ‘--q 20 --phred33 --stringency 5 --length 20 --paired’.	Trim Galore suggested: (Trim Galore, RRID:SCR_011847)
   SAMtools (v1.3.1) was used to sort bam files by genomic coordination and make a bam file index.	SAMtools suggested: None
   PCR duplicates were removed using Picard (v2.23.3).	Picard suggested: (Picard, RRID:SCR_006525)
   Methylation profiles were calculated by deeptools (v3.5.1) (Ramirez et al., 2014)	deeptools suggested: (Deeptools, RRID:SCR_016366)
   Differentially methylated regions (DMRs) by methylKit: The R package methylKit (v1.14.2) (Akalin et al., 2012) was used to identify DMRs between healthy and recovery groups.	methylKit suggested: (methylKit, RRID:SCR_005177)
   The bulk RNA-seq and WGBS data generated during this study is available in Genome Sequence Archive (GSA) for human data repository of National Genomics Data Center	Genome Sequence Archive suggested: None
   r (BioProject No. PRJCA006301, https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA006301).	BioProject suggested: None

   ---

   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.

   ---

   Results from scite Reference Check: We found no unreliable references.

   ---

   Read the original source
3. 

   Version published to 10.1101/2022.04.19.22274029 on medRxiv

   Apr 23, 2022