Cargando…

Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq

It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0,...

Descripción completa

Detalles Bibliográficos
Autores principales: Ilgisonis, Ekaterina V., Ponomarenko, Elena A., Tarbeeva, Svetlana N., Lisitsa, Andrey V., Zgoda, Victor G., Radko, Sergey P., Archakov, Alexander I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9760921/
https://www.ncbi.nlm.nih.gov/pubmed/36545510
http://dx.doi.org/10.3389/fmolb.2022.944639
_version_ 1784852590436024320
author Ilgisonis, Ekaterina V.
Ponomarenko, Elena A.
Tarbeeva, Svetlana N.
Lisitsa, Andrey V.
Zgoda, Victor G.
Radko, Sergey P.
Archakov, Alexander I.
author_facet Ilgisonis, Ekaterina V.
Ponomarenko, Elena A.
Tarbeeva, Svetlana N.
Lisitsa, Andrey V.
Zgoda, Victor G.
Radko, Sergey P.
Archakov, Alexander I.
author_sort Ilgisonis, Ekaterina V.
collection PubMed
description It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for various types of biological material was carried out, and the HepG2 cell line transcriptome was compared with the transcriptome of liver tissue cells. In addition, the contribution of variability in the coverage of expressed genes in human transcriptomes to the creation of a draft human transcriptome was evaluated. For human liver tissues, ONT makes an extremely insignificant contribution to the overall coverage of the transcriptome. Thus, to ensure maximum coverage of the liver tissue transcriptome, it is sufficient to apply only one technology: Illumina RNA-Seq (FPKM > 0).
format Online
Article
Text
id pubmed-9760921
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-97609212022-12-20 Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq Ilgisonis, Ekaterina V. Ponomarenko, Elena A. Tarbeeva, Svetlana N. Lisitsa, Andrey V. Zgoda, Victor G. Radko, Sergey P. Archakov, Alexander I. Front Mol Biosci Molecular Biosciences It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for various types of biological material was carried out, and the HepG2 cell line transcriptome was compared with the transcriptome of liver tissue cells. In addition, the contribution of variability in the coverage of expressed genes in human transcriptomes to the creation of a draft human transcriptome was evaluated. For human liver tissues, ONT makes an extremely insignificant contribution to the overall coverage of the transcriptome. Thus, to ensure maximum coverage of the liver tissue transcriptome, it is sufficient to apply only one technology: Illumina RNA-Seq (FPKM > 0). Frontiers Media S.A. 2022-12-05 /pmc/articles/PMC9760921/ /pubmed/36545510 http://dx.doi.org/10.3389/fmolb.2022.944639 Text en Copyright © 2022 Ilgisonis, Ponomarenko, Tarbeeva, Lisitsa, Zgoda, Radko and Archakov. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Ilgisonis, Ekaterina V.
Ponomarenko, Elena A.
Tarbeeva, Svetlana N.
Lisitsa, Andrey V.
Zgoda, Victor G.
Radko, Sergey P.
Archakov, Alexander I.
Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq
title Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq
title_full Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq
title_fullStr Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq
title_full_unstemmed Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq
title_short Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq
title_sort gene-centric coverage of the human liver transcriptome: qpcr, illumina, and oxford nanopore rna-seq
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9760921/
https://www.ncbi.nlm.nih.gov/pubmed/36545510
http://dx.doi.org/10.3389/fmolb.2022.944639
work_keys_str_mv AT ilgisonisekaterinav genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq
AT ponomarenkoelenaa genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq
AT tarbeevasvetlanan genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq
AT lisitsaandreyv genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq
AT zgodavictorg genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq
AT radkosergeyp genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq
AT archakovalexanderi genecentriccoverageofthehumanlivertranscriptomeqpcrilluminaandoxfordnanoporernaseq