Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and...

Area of Science:

• * Molecular Biology
• * Genomics
• * Transcriptomics

Background:

• * Ectopic expression of RUNX3 or ZBTB46 transcription factors induces phenotypic and developmental changes in mouse embryonic stem cell (ESC)-derived progenitors.
• * Understanding the gene expression profiles regulated by these transcription factors is crucial for deciphering their roles.

Purpose of the Study:

• * To evaluate and compare two next-generation sequencing technologies for transcriptome profiling.
• * To assess the suitability of the DNBSEQ G400 (MGI) and NextSeq 500 (Illumina) platforms for gene expression analysis.
• * To identify differentially expressed genes regulated by RUNX3 and ZBTB46.

Main Methods:

• * RNA sequencing (RNA-seq) was performed on murine ESCs with ectopic expression of RUNX3 or ZBTB46.
• * Comparison of DNA nanoball-based DNBSEQ G400 (MGI) with bridge-PCR-based NextSeq 500 (Illumina).
• * Evaluation of two MGI sequencing reagent types (Standard vs. Hot-massive parallel sequencing (MPS)) on the DNBSEQ G400.

Main Results:

• * Both sequencing platforms demonstrated comparable quality, uniformity, and gene expression profiles.
• * Highly overlapping gene lists regulated by RUNX3 and ZBTB46 were obtained from both platforms.
• * Standard and Hot-MPS reagents on the DNBSEQ G400 also yielded overlapping gene expression data.
• * Identified specific upregulated genes, including *Gzmb*, *Gzmd*, *Gzme*, *Gdf6*, and *Ccr7* for RUNX3, and *Gpx2*, *Tdpoz4*, and *Arg2* for ZBTB46.

Conclusions:

• * Both DNBSEQ G400 and NextSeq 500 are suitable for transcriptome profiling and target gene identification.
• * The DNBSEQ G400 offers a cost-effective alternative for gene expression monitoring.
• * The study provides valuable data for exploring RUNX3- and ZBTB46-dependent gene regulatory networks.