Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics
Iamshchikov Pavel1,2, Larionova Irina3,4, Gerashchenko Tatiana1,5
1Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia.
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.
Related Concept Videos
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
DNA Microarrays
Genomics
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...


