Protocol for quantifying stem-cell-derived cardiomyocyte maturity using transcriptomic entropy score

• Published in: STAR protocols 2024-06, Vol.5 (2), p.103083, Article 103083
• Main Authors: Chen, Elaine Zhelan, Kannan, Suraj, Murphy, Sean, Farid, Michael, Kwon, Chulan
• Format: Article
• Language: English
• Subjects: Bioinformatics; Developmental biology; Gene expression; Protocol; RNA-seq; Stem cells
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2024.103083

The inability to quantify cardiomyocyte (CM) maturation remains a significant barrier to evaluating the effects of ongoing efforts to produce adult-like CMs from pluripotent stem cells (PSCs). Here, we present a protocol to quantify stem-cell-derived CM maturity using a single-cell RNA sequencing-based metric “entropy score.” We describe steps for generating an entropy score using customized R code. This tool can be used to quantify maturation levels of PSC-CMs and potentially other cell types. For complete details on the use and execution of this protocol, please refer to Kannan et al.1 [Display omitted] •Index PSC-CM maturation status using a single-cell RNA sequencing-based metric•Filter out poor-quality cells with quality control metrics for a more reliable comparison•Visualize gene expression trend over entropy scores•Compare entropy scores across different studies Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. The inability to quantify cardiomyocyte (CM) maturation remains a significant barrier to evaluating the effects of ongoing efforts to produce adult-like CMs from pluripotent stem cells (PSCs). Here, we present a protocol to quantify stem-cell-derived CM maturity using a single-cell RNA sequencing-based metric “entropy score.” We describe steps for generating an entropy score using customized R code. This tool can be used to quantify maturation levels of PSC-CMs and potentially other cell types.