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. 2018 Dec 18;9:5375. doi: 10.1038/s41467-018-07787-6

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© The Author(s) 2018

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — Genome-wide binding of SCL, ETO2 and RYBP in FLK1⁺ cells. a SCL ChIP-seq track of Eto2 locus in day 3.5 FLK1⁺ EB cells. Blue arrows, SCL peaks associated to Eto2; red rectangles, ATAC peaks; green rectangles, SCL-bound cis-elements further detailed in Supplementary Fig. 5. b RT-qPCR analyses of Eto2 mRNA expression from WT and Scl^-/- EB differentiation kinetics (day 2–day 6) relative to Gapdh. n = 3–5, mean ± SD; student’s t-test *p < 0.05. c Western blot analysis of day 4.5 WT EB nuclear extracts immunoprecipitated (IP) with anti-SCL antibodies. Members of SCL complex are detected as indicated. n = 3. d Overlap between SCL and ETO2 ChIP-seq peaks. e Overlap between SCL-bound and ETO2-bound genes. 352 of these are SCL direct DEGs. f SCL ChIP-seq track of Rybp, Pcgf5 and Ring1b loci in day 3.5 FLK1⁺ EB cells. Blue arrows, SCL peaks associated to the genes; red rectangles, ATAC peaks; green rectangles, SCL-bound cis-elements further detailed in Supplementary Fig. 5. g RT-qPCR analyses of Rybp, Pcgf5 and Ring1b mRNA expression from WT and Scl^-/- EB differentiation kinetics (day 2–day 6) relative to Gapdh. n = 3–5, mean ± SD; student’s t-test *p < 0.05. h Western blot analysis of day 4.5 WT EB nuclear extracts immunoprecipitated (IP) with anti-SCL antibodies (top), -RYBP (bottom, left) and -RING1B (bottom, right) antibodies. Members of PRC1 complex (RING1B, RYBP) and SCL complex (LMO2, ETO2) are detected as indicated. Asterisk (*) indicates heavy or light IgG chain. White arrow indicates SCL band in RING1B IP. i Overlap between SCL and RYBP ChIP-seq peaks. j Overlap between SCL-bound and RYBP-bound genes. Seven hundred and ten of these are SCL direct DEGs. k Overlap between SCL-bound, ETO2-bound, and RYBP-bound 778 SCL direct DEGs. Number and representative examples of SCL direct target genes in the four categories defined by SCL, ETO2, and RYBP binding are shown. l UCSC tracks showing SCL, ETO2 and RYBP binding on examples of activated and repressed SCL direct DEGs in the four categories defined by SCL, ETO2, and RYBP binding. See also Supplementary Figs. 4–6 and 9, Supplementary Data 3