A PLURIPOTENT STEM CELL PLATFORM FOR in VITRO SYSTEMS GENETICS STUDIES of MOUSE DEVELOPMENT

The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for understanding genotype-phenotype relationships and modeling polygenic traits and disorders. Here, we establish a genetic reference panel of naïve and primed PSCs (n = 250) from the Diversity Outbred (DO) mouse stock to enable high resolution quantitative trait locus mapping of molecular phenotypes in developing cellular systems. These data, methods, and cellular resources provide a roadmap for population-scale studies to dissect the genetic basis of complex traits that will complement and empower similar studies in human populations. Ultimately, our objective is to use the panel of genetically distinct DO PSC lines to precisely measure how genetic variants in populations modulate molecular features of pluripotency and directed differentiation using single cell genomics. Instead of individually phenotyping each cell line, pooled cell culture (“cell villages”) has been implemented in human PSCs to analyze cellular phenotypes at scale with reduced technical variability and lower material and labor costs. To evaluate a cell pooling strategy for DO PSCs, we selected 76 distinct EpiSC lines including 49 male and 24 female lines (n=2 sex genotype XO, n=1 sex genotype undetermined) (Fig. 4A). We thawed 15 pools of 5-6 DO PSCs each and cultured them in parallel for 48 hours. We then combined a total of 30,000 cells from 5 distinct pools in equal proportion for single-cell RNA-sequencing across four lanes (n=28-30 total cell lines per sequencing lane). In total, we sequenced 120,000 cells targeting a depth of 40,000 reads per cell (Fig. 4A). We generated a pipeline to impute each donor’s full genome and output VCF genotype files for compatibility with Dropulation. The Dropulation pipeline was adjusted for use with the GRCm38 mouse genome assembly to assign the most likely donor genotype to each cell and perform doublet detection.