Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to un...

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Autores principales:	Mikhail A. Pyatnitskiy, Viktoriia A. Arzumanian, Sergey P. Radko, Konstantin G. Ptitsyn, Igor V. Vakhrushev, Ekaterina V. Poverennaya, Elena A. Ponomarenko
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	transcriptomics nanopore technology RNA-seq MinION pathway activation systems biology Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/169759de0b984a4e87823b821fcc24e6
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spelling	oai:doaj.org-article:169759de0b984a4e87823b821fcc24e62021-11-25T16:47:19ZOxford Nanopore MinION Direct RNA-Seq for Systems Biology10.3390/biology101111312079-7737https://doaj.org/article/169759de0b984a4e87823b821fcc24e62021-11-01T00:00:00Zhttps://www.mdpi.com/2079-7737/10/11/1131https://doaj.org/toc/2079-7737Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to unravel activated biological processes responsible for disease progression and response to therapies. This trend is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether gene abundances measured by MinION direct RNA sequencing are suited to produce robust estimates of pathway activation for single sample scoring methods. We performed multiple RNA-seq analyses for a single sample that originated from the HepG2 cell line, namely five ONT replicates, and three replicates using Illumina NovaSeq. Two pathway scoring methods were employed—ssGSEA and singscore. We estimated the ONT performance in terms of detected protein-coding genes and average pairwise correlation between pathway activation scores using an exhaustive computational scheme for all combinations of replicates. In brief, we found that at least two ONT replicates are required to obtain reproducible pathway scores for both algorithms. We hope that our findings may be of interest to researchers planning their ONT direct RNA-seq experiments.Mikhail A. PyatnitskiyViktoriia A. ArzumanianSergey P. RadkoKonstantin G. PtitsynIgor V. VakhrushevEkaterina V. PoverennayaElena A. PonomarenkoMDPI AGarticletranscriptomicsnanopore technologyRNA-seqMinIONpathway activationsystems biologyBiology (General)QH301-705.5ENBiology, Vol 10, Iss 1131, p 1131 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	transcriptomics nanopore technology RNA-seq MinION pathway activation systems biology Biology (General) QH301-705.5
spellingShingle	transcriptomics nanopore technology RNA-seq MinION pathway activation systems biology Biology (General) QH301-705.5 Mikhail A. Pyatnitskiy Viktoriia A. Arzumanian Sergey P. Radko Konstantin G. Ptitsyn Igor V. Vakhrushev Ekaterina V. Poverennaya Elena A. Ponomarenko Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
description	Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to unravel activated biological processes responsible for disease progression and response to therapies. This trend is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether gene abundances measured by MinION direct RNA sequencing are suited to produce robust estimates of pathway activation for single sample scoring methods. We performed multiple RNA-seq analyses for a single sample that originated from the HepG2 cell line, namely five ONT replicates, and three replicates using Illumina NovaSeq. Two pathway scoring methods were employed—ssGSEA and singscore. We estimated the ONT performance in terms of detected protein-coding genes and average pairwise correlation between pathway activation scores using an exhaustive computational scheme for all combinations of replicates. In brief, we found that at least two ONT replicates are required to obtain reproducible pathway scores for both algorithms. We hope that our findings may be of interest to researchers planning their ONT direct RNA-seq experiments.
format	article
author	Mikhail A. Pyatnitskiy Viktoriia A. Arzumanian Sergey P. Radko Konstantin G. Ptitsyn Igor V. Vakhrushev Ekaterina V. Poverennaya Elena A. Ponomarenko
author_facet	Mikhail A. Pyatnitskiy Viktoriia A. Arzumanian Sergey P. Radko Konstantin G. Ptitsyn Igor V. Vakhrushev Ekaterina V. Poverennaya Elena A. Ponomarenko
author_sort	Mikhail A. Pyatnitskiy
title	Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
title_short	Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
title_full	Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
title_fullStr	Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
title_full_unstemmed	Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
title_sort	oxford nanopore minion direct rna-seq for systems biology
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/169759de0b984a4e87823b821fcc24e6
work_keys_str_mv	AT mikhailapyatnitskiy oxfordnanoporeminiondirectrnaseqforsystemsbiology AT viktoriiaaarzumanian oxfordnanoporeminiondirectrnaseqforsystemsbiology AT sergeypradko oxfordnanoporeminiondirectrnaseqforsystemsbiology AT konstantingptitsyn oxfordnanoporeminiondirectrnaseqforsystemsbiology AT igorvvakhrushev oxfordnanoporeminiondirectrnaseqforsystemsbiology AT ekaterinavpoverennaya oxfordnanoporeminiondirectrnaseqforsystemsbiology AT elenaaponomarenko oxfordnanoporeminiondirectrnaseqforsystemsbiology
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Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

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