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. 2023 Oct 20;24:239. doi: 10.1186/s13059-023-03077-7

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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/. 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 in a credit line to the data.

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Fig. 4 — Method of mRNA enrichment affects gene expression profile. A A principal component analysis of the rRNA^- Dissociated and polyA⁺ Dissociated bulk samples, where color indicates patient of origin and shape indicates whether samples were poly-A captured or rRNA depleted. Two points that are close together on the PCA plot are similar in their expression profiles. B A volcano plot of the differential expression results based on mRNA enrichment method, with gene sets of interest colored: histones, other non-polyadenylated genes [53], and mitochondrial genes. C Combined expression of all histone genes in each sample based on mRNA enrichment method. D Combined expression of all mtDNA genes based on mRNA enrichment method