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. 2019 Jan 21;10:360. doi: 10.1038/s41467-018-08126-5

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© The Author(s) 2019

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. 4 — Enhancer analysis at single-cell resolution. Comparison of enhancers detected by bulk CAGE and pooled C1 CAGE data a showing bidirectional read profiles smoothed by generalized additive model and b epigenetic profiles. c Bidirectionality scores (0: equally bidirectional; 1: fully unidirectional) at selected enhancers for pooled cells downsampled to the same depth as corresponding single cells 100 times (red dots: mean, black bars: standard error) and single-cells (blue dots: mean; black bars: standard error). d Example locus on chromosome 12: read profile histogram (upper box), and read presence or absence in single-cells (lower box). e–g Comparison of enhancers and gene promoters in C1 CAGE and bulk CAGE: e fraction of bulk features detected within each cell, stratified by bulk expression level, centre line = median, box = 25th to 75th percentiles, whiskers = up to 1.5× interquartile range from the box. f Density plots of the maximum expression levels, g Gini coefficient distribution in single-cell data. Lower scores: broad expression (expressed in more cells); higher scores: more specific/enriched expression (fewer cells). Source data are provided as a Source Data file