Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

BACKGROUND: The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics. RESULTS: The performed comparison demonstrates that GeneMind Genolab M sequencing platform produces highly consistent with Illumina NextSeq 2000 sequencing results. Both platforms have similar performance in terms of sequencing quality and detection of UMI, spatial barcode, and probe sequence. Raw read mapping and following read counting produced highly comparable results that is confirmed by quality control metrics and strong correlation between expression profiles in the same tissue spots. Downstream analysis including dimension reduction and clustering demonstrated similar results, and differential gene expression analysis predominantly detected the same genes for both platforms. CONCLUSIONS: GeneMind Genolab M instrument is similar to Illumina sequencing efficacy and is suitable for 10x Genomics Visium spatial transcriptomics. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09192-w.