Extended Data Fig. 10: Limits of precision in scaled gene expression profiles.
From: Precise and scalable self-organization in mammalian pseudo-embryos
a: Normalized mean expression profiles for each gene (SOX2, CDX2, BRA and FOXC1) of all gastruloids of different \({\overline{N}}_{0}\). For each gene, positional markers are defined at three positions corresponding to the 25% (\({x}_{25}\), blue), 50% (\({x}_{50}\), black), and 75% (\({x}_{75}\), red) of maximum profile intensity levels (vertical dashed lines), respectively. b: Absolute positions of the 25%, 50% and 75% maximum intensity levels for each gastruloid (same as in Fig. 4c) as a function of gastruloid length (same color code as above). Perfect scaling would imply \({R}^{2}=1\), meaning that 100% of the observed boundary position variance is related to gastruloid length. Slope values correspond to the average position of the three positional markers in relative units \({x}_{p}/L\). c: Relative position of the 25%, 50% and 75% maximum intensity levels as a function of L for each gastruloid (same color code as above). Perfect scaling predicts statistical independence of the relative boundary position (50% maximum intensity position) and the absolute gastruloid length. We performed a linear regression and found that the slopes are statistically different from zero (see Table S9 for p-values), with a 99% confidence interval; see slopes in legend. A slope of \({10}^{-5}\) μm−1 means that a decrease or an increase of 300 μm around the case \({\overline{N}}_{0}=300\) leads to a shift of the positional marker of ∼1% along the AP midline, that is ∼6 μm (\(\le 1{d}_{c}\)). A slope of \({10}^{-4}\) μm−1 (as is the case for BRA) means that a decrease or an increase of 300 µm leads to a shift of the positional marker of ∼10% along the AP midline, that is ∼60 μm (∼4\({d}_{c}\)). For \({x}_{50}/L\), the slopes for the four genes SOX2, CDX2, BRA, and FOXC1 are 2.8 ± 1 10−5, 3.4 ± 1 10−5, 2.0 ± 2 10−5 and 2.9 ± 3 10−5 μm−1, respectively. d: Positional error for the three markers (same color code as above) converted in cell diameter units (\({d}_{c}\)) as a function of average gastruloid length for the four genes SOX2, CDX2, BRA, and FOXC1. The range of gastruloid lengths is binned; each data point corresponds to the bin average. The positional error remains between 1–2 cells for all genes and all markers within a certain length range (up to 600 μm for FOXC1, up to 800 μm for the other genes). This range corresponds to the mean length of gastruloids in a range \(100\le {\overline{N}}_{0}\le 500\) for each experiment (Extended Data Fig. 9b). See Table S5 for sample numbers.
