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. 2019 Dec 30;7:222. doi: 10.1186/s40478-019-0871-7

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 5 — Whole-transcriptome analysis reveals impaired development in CLN3^Q352X cerebral organoids. a Heatmap clustering the differentially expressed genes between Control (healthy) and CLN3^Q352X (mutant) brain organoids. b Gene enrichment analysis of CLN3^Q352X network. Genes that are upregulated in disease phenotype were significantly enriched in cellular processes highlighted in green, while downregulations are depicted in red. c Pathway enrichment analysis of the CLN3^Q352X network. Pathway up-regulations are highlighted in green, while down-regulations are marked in red. d Log 2 Fold change expression values for genes related to brain development and cortical morphogenesis were generally decreased in CLN3^Q352X. e Log 2 Fold change expression values for genes related to synapses, which were mostly downregulated in the CLN3^Q352X organoids. Genes in D and E are specifically differentially in our dataset (but not necessarily present in the networks) and belong to the pathways extracted from Pathway unification database (PathCards)