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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. 5 — a Variation in differentiation efficiency across cell lines. Left: Differentiation progress over time, showing trajectories for 98 cell lines, coloured by differentiation efficiency. Shown are 98 cell lines with sufficient data at all time points (out of 126, more than 10 cells). Differentiation efficiency of a cell line was defined as the average pseudotime across all cells on day 3. Right: Differentiation efficiency across cell lines (points), and consistency of individual cell lines differentiated in multiple experiments (vertical bars). b Associations between iPSC gene expression levels and differentiation efficiency. Left: schematic. Centre: Genome-wide analysis to identify markers of differentiation efficiency, considering iPSC gene expression levels. Displayed are negative log P-values signed by the direction of the effect. Horizontal blue lines denote FDR = 10% (Benjamini-Hochberg adjusted). Autosomal genes with significant associations are shown in blue; X chromosome genes with significant associations are shown in red. Right: Scatter plot between gene expression in the iPS state and differentiation efficiency for the X chromosome gene ZDHHC9.