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. 2023 Jun 26;14:3795. doi: 10.1038/s41467-023-39011-5

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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. 3 — A Volcano plots displaying gene expression Log2 fold changes and their respective statistical score (p value) of negative LNA GapmeR control (NC) vs LNA GapmeR targeting MALAT1 (LNA-MALAT1) or NEAT1 (LNA-NEAT1) transfected differentiated HEKn cells. Differential expression analysis was carried out using DESeq2 package. Volcano plot was generated with Enhanced Volcano R package and statistical analyses were carried out using R software. P = FDR (False Discovery Rate) adjusted p value. B Venn diagram showing the shared downregulated genes and upregulated genes in LNA-NEAT1 or LNA-MALAT1 transfected HEKn cells. C Barplot showing the top gene ontology (GO) terms for Biological Process of the downregulated genes upon LNA-NEAT1 transfection of differentiated HEKn cells. GO terms were ordered by FDR (False Discovery Rate) adjusted p value calculated by ShinyGO version 0.76. D Heatmap showing the unsupervised hierarchical clustering of genes associated to the top GO terms in negative control (NC, green) or LNA-NEAT1 (violet) transfected differentiated HEKn cells. Color scheme: yellow (highest) blue (lowest) VSD score. E GSEA of genes downregulated in NEAT1 depleted keratinocytes against a calcium-differentiated keratinocyte gene set (GSE18590). F Bar plot showing the top GO DISEASE terms of genes downregulated in NEAT1 depleted keratinocytes. GO terms were ordered by FDR (False Discovery Rate) adjusted p value calculated by ShinyGO version 0.76. G GSEA of LNA-NEAT1 downregulated genes set against three keratinocytes differentiation signatures resulted by p63 (GSE33495), ZNF750 (GSE32685) or KLF4 (GSE32685) depletion. H IPA Upstream regulator analysis of NEAT1 profile RNA.