Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq.
Illumina RNA-Seq
Oxford Nanopore Technologies MinION
human genome
qPCR
transcriptomics
Journal
Frontiers in molecular biosciences
ISSN: 2296-889X
Titre abrégé: Front Mol Biosci
Pays: Switzerland
ID NLM: 101653173
Informations de publication
Date de publication:
2022
2022
Historique:
received:
15
05
2022
accepted:
10
11
2022
entrez:
22
12
2022
pubmed:
23
12
2022
medline:
23
12
2022
Statut:
epublish
Résumé
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).
Identifiants
pubmed: 36545510
doi: 10.3389/fmolb.2022.944639
pii: 944639
pmc: PMC9760921
doi:
Types de publication
Journal Article
Langues
eng
Pagination
944639Informations de copyright
Copyright © 2022 Ilgisonis, Ponomarenko, Tarbeeva, Lisitsa, Zgoda, Radko and Archakov.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Biol Direct. 2016 Dec 20;11(1):66
pubmed: 27993156
J Proteome Res. 2016 Nov 4;15(11):4030-4038
pubmed: 27527821
BMC Bioinformatics. 2010 Feb 18;11:94
pubmed: 20167110
Proteomics. 2011 May;11(10):1853-6
pubmed: 21563312
Biomed Khim. 2017 Mar;63(2):147-153
pubmed: 28414286
J Proteome Res. 2014 Jan 3;13(1):183-90
pubmed: 24328317
J Proteome Res. 2013 Jan 4;12(1):123-34
pubmed: 23256950
Science. 1960 Oct 21;132(3434):1115-8
pubmed: 17790723
Nat Commun. 2019 Jul 31;10(1):3359
pubmed: 31366910
Front Genet. 2021 Jun 14;12:674534
pubmed: 34194472
Genome Biol. 2016 Nov 25;17(1):239
pubmed: 27887629
RNA. 2020 Aug;26(8):903-909
pubmed: 32284352
J Cheminform. 2015 May 20;7:20
pubmed: 26052348
Rev Sci Instrum. 1948 May;19(5):323-30
pubmed: 18865831
Data Brief. 2021 May 12;36:107130
pubmed: 34095379
J Proteome Res. 2017 Dec 1;16(12):4311-4318
pubmed: 28956606
Int J Anal Chem. 2016;2016:7436849
pubmed: 27298622