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. 2020 Dec 14;10:21900. doi: 10.1038/s41598-020-79082-8

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Limited differences in gene expression between ECO and ICO. Gene expression analysis of three paired ICO and ECO and one additional ICO line was performed using RNAseq. Selected genes, as described by Aizarani et al.¹⁵ that are expressed in EpCAM-positive cells and associated with progenitors, hepatocyte-fate or cholangiocyte-fate. Shown are normalized (bulk) RNA sequencing results of the undifferentiated ECO and ICO for this specific gene set. Expression of the progenitor, hepatocyte-fate- and cholangiocyte-fate associated genes was similar between ECO and ICO. The expression heatmap shows Z-scores that are color-coded as shown (A). No significant differences between ICO and ECO for this gene set was observed. The expression heatmap (B) indicates clusters of genes that are differentially expressed (29 in total, p adjusted < 0.05), 13 higher expressed in ECO and 16 higher in ICO. This analysis reveals that although both organoid types are very similar in gene expression profiles, there are some differences albeit in a relatively low number of genes.