Gene expression dynamics underlying cell fate emergence in 2D micropatterned human embryonic stem cell gastruloids

We applied BMP4 to circular micropattern cultures to differentiate human embryonic stem cells (H1 hESCs) into microcolonies termed 'gastruloids', comprising germ layer and extraembryonic cells. Time-course single cell RNA-sequencing was performed at 0h (immediately before BMP4 treatment), 12h, and 24h after BMP4 treatment. Combining these 0h, 12h, and 24h datasets with previously generated 44h datasets, we report transcriptomic dynamics over the course of BMP4-driven differentiation in micropatterned cultures. Overall design: Single-cell RNA sequencing was performed on gastruloid cells differentiated from H1 hESCs at 0h (immediately before BMP4 treatment), 12h, and 24h of BMP4 treatment.