Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types

Embryoid bodies, 3D aggregates of spontaneously differentiating iPSCs, have the potential to be a useful model system for genomic studies of diverse cell types. We first collected single-cell RNA-sequencing data from embryoid bodies (EBs) generated from 3 Yoruba individuals (18858, 18511, and 19160) in 3 replicates. We classify functional heterogeneity in EB cells using unsupervised clustering, differential expression analysis, reference annotation, and topic modelling. We then inferred differentiation trajectories that recapitulate known developmental patterns of gene expression. We later collected Day 21 EBs from a single replicate of 5 additional Yoruba iPSC lines (18856, 18912, 19140,19159, and 19210) and use this data to demonstrate robustness of EB cell type composition across iPSC lines. Our results establish EBs as a powerful model system to facilitate discovery of QTLs for cell type composition, as well as eQTLs and dynamic eQTLs across a multitude of human cell types and developmental trajectories. Overall design: We differentiated iPSCs from 3 Yoruba individuals to Embryoid Bodies in 3 replicates. On day 21 of differentiation, EB cells from all 3 individuals were pooled and single-cell RNA-seq data was collected using the 10x Genomics V3.0 kit. We then differentiated iPSCs from an additional 5 Yoruba individuals. On day 21 of differentiation, EB cells from all 5 individuals were pooled and single-cell RNA-seq data was collected using the 10x Genomics V3.1 kit.