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. 2021 May 28;49(14):e82. doi: 10.1093/nar/gkab423

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — SCEPTRE quantifies one of two histone marks at three genomic regions. (A) Example images of the approximate center plane for each image stack of simultaneously FISH-labeled MYL6, HOXC or LINC-PINT loci (green) from the same expanded RPE1 cell immunolabeled for H3K4me3 marks (K4me3, magenta). (B) Distribution of H3K4me3 fluorescence signals (arb. = arbitrary units) within H3K4me3, randomly selected regions (random), MYL6, HOXC and LINC-PINT clusters (cluster numbers are K4me3 = 390331, random = 7421, MYL6 = 91, HOXC = 135, LINC-PINT = 46). (C) Example images of the approximate center plane for each image stack of simultaneously FISH-labeled MYL6, HOXC or LINC-PINT loci (green) from the same expanded RPE1 cell immunolabeled for H3K27me3 marks (K27me3, magenta). (D) Distribution of H3K27me3 fluorescence signals within H3K27me3, randomly selected regions, MYL6, HOXC and LINC-PINT clusters (cluster numbers are K27me3 = 196 798, random = 6041, MYL6 = 87, HOXC = 85, LINC-PINT = 72). (E) CUT&RUN normalized counts for H3K4me3 (top) or H3K27me3 (bottom) at the FISH-labeled MYL6, HOXC and LINC-PINT regions (highlighted). Significance determined by a right-tailed Wilcoxon rank-sum test of fluorescence signals in each FISH-labeled set against the random cluster distribution. All scale bars are in pre-expansion units.