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. 2024 Apr 15;21(6):974–982. doi: 10.1038/s41592-024-02239-0

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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/.

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Fig. 1 — a, Left, schematics of the LiMCA procedure. Right, the 20-kb resolution 3D genome structure of a representative cell; expressed genes are projected. RT, reverse transcription. b, Comparison of ensemble LiMCA and bulk Hi-C. The maximum intensity is indicated. c, Scatter-plot of the first eigen value between ensemble LiMCA and bulk Hi-C at 100-kb resolution. d, Scatter-plot of expression level (FPKM) between bulk RNA-seq (ENCODE ENCFF897XES) and combined expression profile of LiMCA. e, The median contact number of LiMCA (GM12878, 1.08 million, n = 220; K562, 1.14 million, n = 28; eHAP, 1.30 million, n = 42; BJ, 678,000, n = 32; olfactory, 652,000, n = 411) (left) is compared to HiRES (brain, 304,000, n = 399; embryo, 264,500, n = 300 (random sampled)) and Dip-C (GM12878, 1.45 million, n = 14; brain, 333,000, n = 300 (random sampled); olfactory, 252,000, n = 409). The median detected gene number of LiMCA (GM12878, 7,954, n = 221; K562, 9,806, n = 63; eHAP, 8,588, n = 42; BJ, 8,911, n = 63; olfactory, 4,528, n = 411) (right) is compared to HiRES (brain, 6,966, n = 399; embryo, 4,058, n = 300 (random sampled)), Smart-seq2 (HEK293T, 11,169, n = 35; MEF, 10,173, n = 7) and 10x chromium (olfactory, 3,556, n = 300 (random sampled of this study); GM12878, 2,754, n = 100 (random sampled)). f, Uniform Manifold Approximation and Projection (UMAP) embedding of four profiled cell lines based on gene expression profiles (left) or single-cell A/B values (right). The same cells are connected with lines. g, Contact matrices (left) around NFKB1, representing ensemble Hi-C data of NFKB1-high group (top left) and NFKB1-low (bottom right). Normalized contact frequency plot (right), centered at the NFKB1 upstream enhancer. The green and yellow dot/line indicates the position of the candidate enhancer and the transcription start site (TSS) and the transcription termination site (TTS) of NFKB1, respectively. h, Radial distribution of gene density; nucleus is sliced to 0.01 thickness. The error bands represent the 95% confidence interval (CI). i, Histograms show the distribution of cluster size within 300 nm for expressed genes and random control. Data were analyzed by a two-sided Mann–Whitney U-test.