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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.
Afiliación
  • Ilgisonis EV; Institute of Biomedical Chemistry, Moscow, Russia.
  • Ponomarenko EA; Institute of Biomedical Chemistry, Moscow, Russia.
  • Tarbeeva SN; Institute of Biomedical Chemistry, Moscow, Russia.
  • Lisitsa AV; Institute of Biomedical Chemistry, Moscow, Russia.
  • Zgoda VG; Institute of Biomedical Chemistry, Moscow, Russia.
  • Radko SP; Institute of Biomedical Chemistry, Moscow, Russia.
  • Archakov AI; Institute of Biomedical Chemistry, Moscow, Russia.
Front Mol Biosci ; 9: 944639, 2022.
Article en En | MEDLINE | ID: mdl-36545510
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).
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Front Mol Biosci Año: 2022 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Front Mol Biosci Año: 2022 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Suiza