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. 2023 Oct 26;13:18380. doi: 10.1038/s41598-023-45144-w

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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 licence, and indicate if changes were made. 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/4.0/.

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(A) Mean-Average (MA) plots of log2 fold change versus log2 average expression between the type of culture condition and FFPE samples. Each dot represents a gene. Log2 fold change above 0 indicates genes with upregulated expression, while lower than 0 indicates genes with down-regulation. Red and blue dots indicate genes that significantly differ in gene expression (p-adj < 0.05). (B) Hierarchical clustering heat map of log2 expression levels of most significantly (p-adj < 0.05) expressed genes resulting from RNA sequencing analysis of (Green) 2D cultured cells with FFPE samples (Blue) 3D cultured cells with FFPE samples. Sample data were pooled and normalized with DeSeq2, followed by H-clustering to compute the cluster dendrogram. (C) Principal-component analysis of sample relationship. PCA 1 is 35% and 34% variance for the relationship between 2D/3D with FFPE data. PCA2 is 20% for both. Cell lines for 2D and 3D culture conditions are clustered in one group apart from FFPE clustering. FFPE: Formalin-Fixed Paraffin-Embedded.