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Research into cardiovascular diseases can benefit greatly from single-cell approaches to genomics and cell biology analyses. However, traditional methods for viable cell isolations from heart tissue are complex, time-consuming, and technically challenging, especially so for cardiomyocytes due to their fragility. Single-cell sequencing libraries from heart cells are also difficult to generate on droplet-based microfluidics platforms due to cell size restrictions. Here, we demonstrate the use of the Singulator™ 100 for the isolation of viable mouse heart cells with high yields, using S2 Genomics’ Heart Cell Reagent and Large Cell Isolation Cartridge. In addition, we have connected the workflow to Parse Biosciences’ Evercode WT v2 kit for generation of scRNA-Seq data, showing that the Parse technology can be used to generate sequencing libraries with cardiomyocyte cell-type representation.