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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,...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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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 |
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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 |
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