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. 2024 Nov 20;635(8039):690–698. doi: 10.1038/s41586-024-08172-8

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© The Author(s) 2024, corrected publication 2024

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Extended Data Fig. 4 — (a) Schematic of estimating cell type enrichment with different morphogen usages. (b) This heat map indicates in how many of the 17 iterations scCODA was executed (using each of the 17 regional cell identity as a reference once) the respective morphogen was found to lead to compositional changes with respect to the reference regional cell identity. A morphogen effect was called significant in this consensus approach if it had a significant effect on cell type composition with respect to more than half of the reference cell types. (c) Effect of different morphogens on regional organoid composition in HNOCA. Positive values correspond to a higher abundance of cells from the indicated regional cell identity in cases where the respective morphogen was used in the differentiation protocol. Top: log2-fold-effect sizes of morphogens per regional cell identity as computed by the scCODA model. Bottom: L1-regularized linear model coefficients. The dashed arrows show consistent enrichment/depletion identified by the two methods.