Caliandro, R.; Belluomo, R.; Hanemaaijer-van der Veer, J.; Oostra, R.-J.; van den Hoff, M. J. B.; Boon, R. A.; Gladka, M. M.

While single-cell RNA sequencing (scRNA-seq) has been the first widely adopted single-cell transcriptomic approach, its reliance on fresh tissue samples has substantially limited its applicability to clinically relevant specimen. Single-nucleus RNA sequencing (snRNA-seq) overcomes this constrain by enabling transcriptomic profiling from frozen material. However, isolating high-quality nuclei from frozen cardiac tissue remains technically challenging due to the dense extracellular matrix, complex tissue architecture, and heterogeneous cellular composition of the heart. To address these challenges, numerous nuclei isolation protocols have been adapted and optimized, resulting in substantial methodological heterogeneity across studies. Despite the widespread use of snRNA-seq in cardiac research, a robust and standardized nuclei isolation protocol that consistently yields high-quality nuclei from frozen human heart tissue is still lacking. Here, we present a comprehensive, end-to-end protocol for nuclei isolation from frozen human left ventricle, along with a detailed downstream pipeline for snRNA-seq data analysis. Our hybrid nuclei isolation strategy integrates multiple sequential clean-up steps designed to preserve nuclear integrity and RNA quality prior to sequencing. Compared with commonly used nuclei isolation protocols, this approach yields substantially higher number of nuclei while maintaining comparable numbers of detected genes and counts, even at lower sequencing depth. Adoption of this protocol may reduce technical variability across studies and facilitate more reproducible snRNA-seq analyses of human cardiac tissue.