Fig. 3

Comparisons across genome-wide datasets. a Per-stage Spearman’s correlations across Poly-Ribo-Seq (“FP”), RNA-Seq (“mRNA”), and mass-spectrometry datasets (“E”—early, “M”—mid, “L”—late stages correspondence in Casas-Vila et al. [26]—see “Materials and methods”). “Maternal” datasets correspond to concatenated mature oocyte and activated egg datasets from Kronja et al. [18]. S2-cells correspond to the Aspden et al. 2014 dataset plus new sequencing. Numbers denote Spearman’s rho. b Numbers and translation fates of maternal ribosome-bound canonical ORFs in the maternal-to-zygotic transition. “Constant translation” denotes ORFs detected as translated by our pipeline in both maternal and early embryo datasets (see Fig. 2a). “Poised for translation” denotes ORFs showing maternal ribosome-binding which only appear translated in the early embryo. “Translation down” denotes ORFs with ribosome-binding and translation in the Maternal dataset, which do not appear translated in the early embryo dataset. c Overall correlation between average embryo Poly-Ribo-Seq RPKM and average embryo Mass-Spec imputed LFQ intensities (both datasets are log₂-transformed). All detected ORFs are included in this analysis. Red points and line show the data binned in intervals of 0.1 RPKM. Note that the linear correlation is lost below RPKM = 1 (log₂ = 2) and above RPKM = 1024 (log₂ = 10). d Differential detectability of canonical ORFs between Poly-Ribo-Seq and mass spectrometry techniques. e Differential detectability of short CDSs between Poly-Ribo-Seq and mass spectrometry. f S2-tagging experiments of nine uncharacterized short CDSs showing translation in either cortical or reticular-punctate patterns (FLAG antibody: green, F-actin stained with phalloidin: red. Scale bar denotes 5 μm)