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

Abstract

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 (NGS) technologies. We compared the DNA nanoball (DNB) based MGI DNBSEQ G400 sequencer with the bridge-PCR based Illumina NextSeq 500 instrument. Moreover, we also compared two types of MGI sequencing reagents (Standard- versus Hot-MPS) with the DNBSEQ G400. Importantly, very similar gene expression profile and greatly overlapping RUNX3 and ZBTB46 regulated gene sets were detected with both platforms. Moreover, almost identical gene expression pattern was obtained with the Hot-MPS reagent compared to the Standard-MPS chemistry. This transcriptomic analysis also facilitated the identification of RUNX3 and ZBTB46 regulated genes. For example, we found that Gzmd, Gdf6 and Ccr7 genes were robustly upregulated upon the forced expression of Runx3, on the other hand, Gpx2, Tdpoz4 and Arg2 were induced upon the ectopic expression of Zbtb46. Together these findings demonstrate that the DNBSEQ G400 system is also suitable for global transcript profiling and target gene selection with lower cost.