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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

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, 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 you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. 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-nc-nd/4.0/.

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Extended Data Fig. 10 — (a-c) UMAP of the unintegrated disease-modeling neural organoid atlas, colored by (a) publications, (b) disease status, (c) transferred level-2 annotation from HNOCA, and (d) transferred regional identities from HNOCA. (e) Dot plot shows expression of selected cell type markers in cells with different transferred cell class labels (level-1) from HNOCA. (f) Dot plot shows expression of selected regional markers in the predicted NPCs and neurons in the disease-modeling atlas with different transferred regional identities from HNOCA. In both (e) and (f), sizes of dots represent percentages of cells expressing the gene, and colors of dots represent the average expression levels. (g-j) UMAP of the glioblastoma GBM-2019 data set, colored by (g) samples, (h) predicted cell class labels (level-1) from the HNOCA projection, (i) expression of astrocyte markers GFAP and AQP4, and (j) the AQP4+ population selected for DE analysis with HNOCA. (k-n) UMAP of the fragile X syndrome FXS-2021 data set, colored by (k) samples, (l) predicted cell type annotation (level-2) from the HNOCA projection, (m) expression of dorsal telencephalic cell markers FOXG1, EMX1 and NEUROD6, (n) the dorsal telencephalic NPC and neuron subset for DE analysis with HNOCA. (o) PCA of the scPoli sample embeddings of samples in HNOCA and five additional data sets projected to HNOCA.