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. 2018 Jan 24;9:347. doi: 10.1038/s41467-017-02729-0

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© The Author(s) 2018

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. 4 — RNA-Seq analysis on C9ORF72 mutant MNs. a Heat map and dendrogram depicting hierarchical clustering of RNA sequencing reads from controls (Con-1, Con-2), C9ORF72 mutant (C9-1, C9-3), and C9-3Δ MNs. b Venn diagram depicting identification of differentially expressed genes between two mutant C9ORF72 MNs and control MNs. Central intersect represents 165 dysregulated genes compared to both control and gene-corrected MNs. c Scatter plot showing comparison of transcriptome reads of two independent C9ORF72 mutant MNs and C9-3Δ MNs to controls. Red crosses denote significantly upregulated genes and blue crosses denote significantly downregulated genes (p < 0.05, analysis performed using DESeq2). These dysregulated genes in C9ORF72 mutant MNs are reversed to control levels in C9-Δ MNs. d, e Graph depicting the spread of differentially regulated, upregulated (d), and downregulated (e) genes in mutant C9ORF72 MNs, red star denotes the levels of GluA1. f, g Gene ontology studies on upregulated (f) and downregulated genes (g)