Fig. 1: Experimental design and analytical approaches.
From: A village in a dish model system for population-scale hiPSC studies
a The experimental design to test for the impact of village culture conditions on individual hiPSC lines using scRNA-seq. Phase I compares the impact of the village culture system using fresh samples collected at each site. Phase II investigates whether cryopreservation of village samples impacts individual hiPSC lines. Phase III utilizes all samples to investigate dynamic effects of the hiPSC lines across pseudotime. Each phase utilizes expression matrices that are separated by condition (site for phase I, cryopreservation status for phase II and pseudotime for phase III) as well as covariate matrices for each condition that contain the hiPSC line, replicate and village status. b A linear mixed model is used to estimate the variance of expression for each gene that is explained by each covariate. Those estimates are calculated for each condition in each Phase of the experimental design and used for downstream analyses. c The pseudotime is estimated for the cells from all samples and used in a linear mixed model to identify genetic effects that are dynamic across pseudotime. ×3: samples in triplicate; 10x Genomics: 10x Genomics scRNA-seq capture. All figure parts are representative.
