Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Szilárd Póliska; Chahra Fareh; Adél Lengyel; Loránd Göczi; József Tőzsér; Istvan Szatmari

doi:10.3389/fgene.2023.1275383

Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Front Genet. 2024 Jan 5:14:1275383. doi: 10.3389/fgene.2023.1275383. eCollection 2023.

Authors

Szilárd Póliska¹, Chahra Fareh^{1

2}, Adél Lengyel^{1

2}, Loránd Göczi^{1

3}, József Tőzsér¹, Istvan Szatmari¹

Affiliations

¹ Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
² Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary.
³ Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.

Abstract

Introduction: We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study, we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-seq testing two next-generation sequencing technologies. Methods: We compared the DNA nanoball-based DNBSEQ G400 sequencer (MGI) with the bridge-PCR-based NextSeq 500 instrument (Illumina) for RNA sequencing. Moreover, we also compared two types of MGI sequencing reagents (Standard versus Hot-massive parallel sequencing (MPS)) with the DNBSEQ G400. Results: We observed that both sequencing platforms showed comparable levels of quality, sequencing uniformity, and gene expression profiles. For example, highly overlapping RUNX3- and ZBTB46-regulated gene lists were obtained from both sequencing datasets. Moreover, we observed that the Standard and the Hot-MPS-derived RUNX3- and ZBTB46-regulated gene lists were also considerably overlapped. This transcriptome analysis also helped us to identify differently expressed genes in the presence of the transgenic RUNX3 or ZBTB46. For example, we found that Gzmb, Gzmd, Gzme, Gdf6, and Ccr7 genes were robustly upregulated upon the forced expression of Runx3; on the other hand, Gpx2, Tdpoz4, and Arg2 were induced alongside the ectopic expression of Zbtb46. Discussion: Similar gene expression profile and greatly overlapping RUNX3- and ZBTB46-regulated gene sets were detected with both DNA sequencing platforms. Our analyses demonstrate that both sequencing technologies are suitable for transcriptome profiling and target gene selection. These findings suggest that DNBSEQ G400 represents a cost-effective alternative sequencing platform for gene expression monitoring. Moreover, this analysis provides a resource for exploration of the RUNX3- and ZBTB46-dependent gene regulatory networks.

Keywords: RNA-seq; RUNX3; ZBTB46; embryonic stem cell; genomics; sequencing technology.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by NKFIH K124890 and GINOP-2.3.2-15-2016-00044 PHARMPROT Hungarian Research Funds to IS. This work was also supported by TKP2021-NKTA-34 and GINOP-2.3.4-15-2016-00002 Hungarian Research Funds to SP, and TKP2020-IKA-04 to JT.