A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development
Fig 4
Nanog/Gata6 pattern for different Fgf4 ceasing time.
(a) Single cell gene expression level in different cell stages in baseline simulation. (b) Cell number percentage of DP/Nanog+/Gata6+/DN cells at different 128C (simulation)/ 100C-150C (experiment) stages with different Fgf ceasing time in simulations and experiments. The horizontal dashed line shows the percentage of Nanog+ cells in wild type experiment. (c) Fgf4/Fgfr2 expression levels (log1p transformed) in Nanog+/Gata6+ cells in different cell stages from scRNA-seq data. The vertical bar shows the standard deviation. T-tests were used to compare between Nanog+ and Gata6+ cells the Fgf4 or Fgfr2 expression levels from E4.5 to E6.5. The (t-statistic, two-tailed p-value) for Fgf4 at E4.5, E5.5, and E6.5 are (11.75, <1e-16), (-0.80, 0.43), and (-1.29, 0.20), respectively; and for Fgfr2 at E4.5, E5.5, and E6.5 are (-3.83, 2.2e-4), (-0.27, 0.78), and (-1.37, 0.17), respectively. (d) Gene expression level of Nanog and Gata6 at 128 cell stage if Fgf ceases at 128C and if Fgf is always on. (e) Violin plot of Gata6 level of Nanog+ cell (red) and Nanog level of Gata6+ cell (blue) for simulation where Fgf4 is always on and simulation where Fgf4 ceases at 128 cell stage. The hollow circle shows the median. The t-statistic and two-tailed p-value are 7.44 and 1.7e-12 between the first two columns, and -0.54 and 0.59 between the last two columns.