Transcriptomic analysis of cardiomyocyte differentiation from human induced pluripotent stem cells (hiPSCs) in 2D and 3D culture

Tridimensional cardiac differentiation from hiPSCs has been largely described in the literature. However, the exact impact that 3D culture has throughout the entire process of cardiac differentiation remains poorly defined. We developed a robust and efficient 3D platform for cardiomyocyte differentiation from hiPSCs, based on the temporal modulation of WNT signalling using small molecules. 3D aggregates of hiPSCs were generated by forced aggregation in microwells and subsequently differentiated. In order to determine the differences in gene expression profile due to 3D culture throughout the different stages of cardiac differentiation, we compared transcriptional changes between cells in 3D aggregates and standard 2D monolayer cardiac differentiation. Analysis of these data suggests a faster commitment of hiPSCs toward the cardiac lineage and also higher degree of cardiomyocyte functional maturation after 20 days of culture in the 3D aggregates when compared with the 2D monolayer. Overall design: Cells from different time points of cardiac differentiation (day 0, 1, 3, 5, 7, 9, 12, 15, 18 and 20), from 3D and 2D culture conditions were collected for RNA-seq. Three biological replicates were obtained for each time point. Deep sequencing was performed in the Illumina platform.