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. 2023 Jan 11;14:156. doi: 10.1038/s41467-022-35487-9

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© The Author(s) 2023

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. 6 — a A diagram showing the workflow of intestinal organoid culture, media treatments, sample preparation, and RNAseq. The figure was created with BioRender.com. b Principal component analysis (PCA) of RNAseq results from the indicated organoids. Each point represents individual samples, and sample groups are indicated by using different colors as indicated in the legend provided. c Venn diagram showing overlap in differentially expressed genes (DEGs) between the indicated conditions. Numbers of DEGs upregulated and downregulated are shown in red and black, respectively. FDR < 0.05 and fold change >1.5 were used to acquire the list of DEGs. Overlapping DEGs from SCM and Wnt5a treated organoids were further divided into two groups by Ptk7 dependency. d Transcription factor enrichment analysis of common DEGs from (c) using i-cisTarget. Highly enriched motifs and predicted transcription factors for Ptk7-dependent and independent DEGs were ranked by normalized enrichment score (NES). e Heatmap showing expression of selected Ptk7-dependent DEGs with TEADs binding motifs in different conditions. Heatmaps of Ptk7-dependent DEGs with different TEAD binding motifs (TEAD 1–4) are found in Supplementary Fig. 6a–d. See also Fig. S6.