Fig. 3

Fig. 3 Differences in zygotic mRNA accumulation between genes and cell types.

A Mean percent of zygotic mRNA per gene across all cells that express it with 3 or more UMI counts (y-axis). Genes were divided into 10 bins with an equal number of genes (x-axis). Since the fraction of zygotic mRNA per gene was equal (0%) for transcripts in the lowest two bins, they are plotted as a single set, which is double in size. The central dot is the median; gray box bounds are 25th and 75th percentiles, upper and lower limits of whiskers are 1.5x interquartile ranges. Values outside of the upper and lower limits are defined as outliers, n = 618 genes per bin. We consider genes in the top two bins as zygotic (blue, zygotic mRNA fraction >65%) and genes in the bottom three bins as maternal (red, zygotic mRNA fraction <5%, first 2 bins are plotted as a single bin). B Expression of genes across 8226 collected single cells. All cells are plotted, and each cell is colored by the normalized expression of a gene’s pre-existing (maternal) copies (red, left map) or newly-transcribed (zygotic) copies (blue, right map). Color scale is gene-specific, and scaled by its maximal total expression and its minimal 30% quantile of maternal and zygotic expression. C A set of 154 genes (rows) with either zygotically or maternally restricted expression within cell-types. Grayscale represents p values for maternal (left column) or zygotic (middle column) mRNA enrichment within cell-type (indicated on left). Right column is colored by % zygotic mRNA (red: <5%, maternal, 5 genes; blue: >65%, zygotic, 129 genes; black: maternal-zygotic, 20 genes). Maternal-zygotic genes can be cell-type restricted in only one of the two components of their expression (e.g., cth1 and pfn1 are only cell-type restricted by their zygotic mRNA, while their maternal mRNA is not restricted). D Single cell expression (as in B) of maternal-zygotic genes with cell-type-restricted zygotic expression. E Single-cell expression (as in B) of genes with cell-type-restricted maternal expression in enveloping layer cells.