Fig. 5: Integration with single-cell CoTACIT multimodal profiles predicts chromatin states that prime the first cell-fate sorting towards ICM and TE cells.
From: Genome-coverage single-cell histone modifications for embryo lineage tracing
a, A computational pipeline for constructing a random forest training model to identify classifier bins associated with lineage specification. b, Receiver operating characteristic of the random forest model. c, Fraction of classifier bins (n = 780) overlapping with ICM and TE differential expressed genes (DEGs). d, Heatmap displaying chromatin-state annotations in all 780 classifier bins. The 780 classifier bins were grouped into four clusters using k-means clustering. e, TF motifs identified during ICM or TE lineage specification. TF motifs with high enrichment (–log10(P) > 5) and expression (reads per kilobase million (RPKM) > 1.5 in Ribo-lite data) along lineage specification are highlighted in bold (for TE) or underline (for ICM). P values were calculated using one-sided binomial tests. f, Quantification of early embryo development from 36 to 108 h. Sample sizes are as follows: control (37, 40, 24), NANOG (35, 22, 29), ZFX (25, 25, 33), HNF4A (38, 26, 24), YY2 (44, 25, 35), TCF12 (33, 34, 21), CEBPB (14, 37, 32), BBX (31, 20, 31), SMAD2 (43, 41, 42), HBP1 (34, 28, 36), CDX2 (34, 29, 41), KLF6 (31, 15, 35), SOX15 (41, 35, 15), MED1 (27, 17, 33), ELF5 (36, 36, 24), HIF1A (24, 14, 40). Data from three replicate experiments are shown for each time point. g, Quantification of morula embryos that develop into normal or abnormal blastocysts. Numbers inside each bar indicate the number of embryos. P values (shown on the chart) were calculated using two-sided Chi-square tests. h, Top, schematic of the two classes of abnormal blastocysts after KD. Bottom, quantification of abnormal blastocysts with SOX2– or CDX2– cell misallocation or the presence of ICM SOX2– cells. The total number of blastocysts is shown. P values were calculated using two-sided G-tests. i, Immunofluorescence staining of mouse embryos at 108 h after fertilization. Shown are z projection 3D images and single-section immunofluorescence images. Representative images out of three independent experiments are shown. Asterisks, adjacent embryos; white arrowheads, CDX2+SOX2+ cells; green arrowheads, misallocated CDX2+ cells. Scale bar, 100 μm.
