Extended Data Fig. 5: Quality controls in generation of synthetic cells.
From: Genome-coverage single-cell histone modifications for embryo lineage tracing
(a) Combined UMAP visualization of the scRNA-seq dataset from this study (n = 1012) and data from by Deng et al.35. Each dot represents an individual cell and is colored by technologies (left) or stages (right). (b) Heatmap showing the Spearman correlation coefficients between H3K4me3 TACIT cells and RNA synthetic cells at each developmental stage. (c) Violin plots showing Spearman correlation coefficients between H3K27ac profiles from TACIT and CoTACIT that are linked to the same scRNA-seq synthetic cells after integration analysis. Box plots centre lines indicate the median, box limits indicate the first and third quartiles, and whiskers indicate 1.5× IQR.The TACIT cell number for each stage is below: 2-cell (66), 4-cell (72), 8-cell (89), morula (121), and blastocyst (166). The CoTACIT cell number for each stage is below: 2-cell (52), 4-cell (70), 8-cell (118), morula (190), and blastocyst (197). (d) UMAP visualization of interpolated single cells on the basis of histone modifications. (e) Hierarchical clustering of synthetic cells from 2-cell, 4-cell, 8-cell, morula and blastocyst embryos. (f) Heatmap showing Pearson correlation of epigenetic profiles for synthetic cells at zygote, 2-cell, 4-cell and 8-cell stages. Correlation coefficients are labeled on the plots. (g) Track view showing aggregated TACIT data of all six histone modifications in 2cell_2 and 4cell_4. (h) Scatter plots showing Spearman correlation between H3K4me3 and H3K27ac signals in synthetic cells at 2-cell and 4-cell stages. Histone modification signals were calculated in ±50 kb regions flanking the TSS of genes exclusively expressed in early-stage embryos. (i) Comparison between H3K27ac and H3K27me3 profiles based on genome-wide distribution for synthetic cells across different developmental stages. Each line represents one synthetic cell. (j) Comparison between H3K27ac and H3K27me3 profiles based on signals in peak regions for synthetic cells across different developmental stages. Each line represents one synthetic cell.
