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. 2020 Feb 10;11:810. doi: 10.1038/s41467-020-14457-z

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Overview of the experimental design. iPSC lines from 125 genotyped donors were pooled in sets of 4-6, across 28 experiments, followed by differentiation towards definitive endoderm. Cells were sampled every 24 h (Methods) and molecularly profiled using scRNA-seq and FACS. https://github.com/ebiwd/EBI-Icon-fonts by EBI Web Development is licensed under CC BY 4.0. b Variance component analysis of 4,546 highly variable genes, using a linear mixed model fit to individual genes to decompose expression variation into time point of collection, cell line and experimental batch (Methods). c Top: Principal component analysis of gene expression profiles for 36,044 QC-passing cells. Cells are coloured by the time point of collection. Bottom: Cells are ordered by pseudotime, defined as the first principal component (PC1). From left to right, cells transition from a pluripotent state to definitive endoderm. d Single cell expression (y-axis) of selected markers for each developmental stage, spanning iPSC (NANOG), mesendo (T), and defendo (GATA6) stages, plotted along pseudotime (x-axis).