High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human embryonic stem cell gastruloid cultures

We used circular micropattern cultures to differentiate human embryonic stem cells (H1 hESCs) into microcolonies termed ‘gastruloids’, comprising germ layer and extraembryonic cells. Differentiated gastruloids were dissociated and reseeded onto micropatterns in single cells solution to study cell sorting behaviors. We applied single-cell RNA sequencing to examine transcriptomes of gastruloids and reseeded cells. Single-cell RNA sequencing was performed on gastruloid cells differentiated from H1 hESCs after 44 hours of BMP4 treatment in micropatterns, and dissociated gastruloid cells reseeded onto micropatterns for 48 hours.