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. 2024 Oct 29;14:25940. doi: 10.1038/s41598-024-77314-9

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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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Fig. 3 — An analysis of differential gene expression and RNA stability across multiple AML cell lines and time points following decitabine treatment. (a,b) RNA-seq reveals genes with significant changes in (a) gene expression and (b) RNA stability in HL-60 cells following treatment with decitabine vs. DMSO. Data are shown as heatmaps displaying counts (of two replicates) row-normalized into Z-scores, grouped by treatment condition and time. Differential RNA expression was calculated using our Salmon-tximport-DESeq2 pipeline. RNA stability was predicted using the REMBRANDTS algorithm and differential RNA stability was calculated using limma. (c,d) RNA-seq shows varying degrees of concordance of differential (c) gene expression and (d) RNA stability across a panel of six AML cell lines. The correlation analysis was performed on the logFC values from (c) DESeq2 and (d) limma results for cells treated with decitabine vs. DMSO. Data are shown as correlation matrices with Pearson’s correlation coefficients (PCC).