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. 2024 Jan 25;22:17. doi: 10.1186/s12915-024-01827-y

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© The Author(s) 2024

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. 1 — Major axes of variation in DNA methylation data are driven by cell type. Scatterplot (a) of the first two principal components where each point represents a sample (n = 123 samples from 47 donors) and the colour of the point indicates the nuclei fraction. Violin plots for the first 5 principal components (b–f) grouped by nuclei fraction (sample sizes can be found in Additional File 2: Supplementary Table 1). DoubleNeg (NeuNNeg/SOX10Neg; n = 21), IRF8Pos (NeuNNeg/SOX10Neg/IRF8Pos; n = 17), NeuNNeg (NeuNNeg; n = 4), NeuNPos (n = 28), SATB2Neg (n = 6), SATB2Pos (n = 9), SOX6Neg (NeuNPos/SOX6Neg; n = 3), SOX6Pos (NeuNPos/SOX6Pos; n = 4), Sox10Pos (NeuNNeg/SOX10Pos; n = 24), TripleNeg (NeuNNeg/SOX10Neg/IRF8Neg; n = 7)