Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms

Abstract

Transcriptional profiling is a powerful tool commonly used to benchmark stem cells and their differentiated progeny. As the wealth of stem cell data builds in public repositories, we highlight common data traps, and review approaches to combine and mine this data for new cell classification and cell prediction tools. We touch on future trends for stem cell profiling, such as single-cell profiling, long-read sequencing, and improved methods for measuring molecular modifications on chromatin and RNA that bring new challenges and opportunities for stem cell analysis. : In this review, Wells and Choi highlight developments in stem cell transcriptome profiling that are moving the field from descriptive to predictive modelling of stem cell biology. The authors review emergence of reference atlas databases for benchmarking new stem cell models, putting together a wish list for future technologies, including single-cell sequencing, that harmonise multi-scaled measurements of stem cell systems. Keywords: pluripotent stem cell, reprogramming, transcriptome, single-cell sequencing, bioinformatics