Extended Data Fig. 8: The relationship between chromatin architecture and gene expression in the cell cycle.
From: Simultaneous profiling of chromatin architecture and transcription in single cells
a, Saddle plots: average contact enrichment between pairs of 100 kb regions arranged by their compartment scores in the different cell cycle phases. b, Uniform manifold approximation and projection (UMAP) embedding showing the clustering of single cells from scCARE-seq 3D chromatin structural profiles. Each dot represents an individual cell and each color represents a cell cluster. c, GO enriched by marker genes of clusters in b. d, Percentage of inter-chromosomal contacts per single mESC in 2i and serum were ordered by cell-cycle phasing and each cell was annotated by cell type colored the same as in a. The black line represents mean trend. Shadow represents the confidence intervals of 0.95. e, Similar to d, Contacts, E-P interactions, UMIs and number of expressed genes per single serum mESCs from left to right. f, Comparison of UMI in single cells of top and bottom group in 2i mESCs. The top and bottom groups were selected based on the top and the bottom each 48 single cells (25%) ranked by number of E-P interactions from highest to lowest. The boxplots were drawn from lower quartile (Q1) to upper quartile (Q3), with the middle line denoting the median, whiskers with maximum 1.5 interquartile range (IQR) and outliers were not indicated. P value, one-sided Wilcoxon signed-rank test. g, Venn diagrams showing the expressed genes in E-P interactions of Early-S and LateS-G2 in e (right). h, Partial gene ontology (GO) terms, enriched by specific genes of Early-S and LateS-G2 in g, respectively.
