Extended Data Fig. 1: Information on generated RNA-seq and Ribo-seq data.

a, Ribosome footprint length distributions across Ribo-seq libraries (nt, nucleotides). b, Fractions of Ribo-seq and RNA-seq reads mapped to 5′-untranslated regions (5′-UTRs), coding sequences (CDSs) and 3′ untranslated regions (3′-UTRs), respectively. c, Distribution of Ribo-seq and RNA-seq reads across the three reading frames in the CDS of dominant splicing isoforms (frame 1: canonical reading frame). d, Mean normalized density of footprints along the coding region of the dominant isoforms of protein-coding genes for the brain Ribo-seq data. The Ribo-seq read (A-site) density for each position is plotted relative to the first nucleotide position of the start codon. e–h, Spearman’s correlation coefficient (ρ) of read counts for protein-coding genes with a mean read count > 1 between the two technical replicates for mouse liver Ribo-seq (e) and RNA-seq (f) data, and for chicken liver Ribo-seq (g) and RNA-seq (h) data. i, Correlations between biological replicates for Ribo-seq and RNA-seq data. Each dot corresponds to Spearman’s correlation coefficient (ρ) in pairs of biological replicates for every species-organ combination. Only one replicate (therefore no pairs) is available for the human liver transcriptome, only two replicates (one pair) are available for the human testis transcriptome and translatome, and only two replicates (one pair) are available for the platypus brain transcriptome. The correlation coefficients between the replicates are similar for the two data types and statistically indistinguishable (P = 0.159) in a Mann–Whitney U test (two-sided). j, Comparisons of gene-expression (rank) changes between the three expression layers. Changes in gene-expression ranks were calculated between expression layers (that is, from transcriptome to translatome, from transcriptome to proteome, and from translatome to proteome), and Spearman’s ρ was calculated to estimate the similarity of rank changes between the different pairs of expression layers. k–n, PCA based on 5,060 robustly expressed (median FPKM > 1 across organ libraries) 1:1 amniote orthologues. Factorial maps represent the relations of PC2 versus PC1 (k), PC3 versus PC1 (l) and PC4 versus PC1 (m). The scree plot (n) indicates the percentage of variance explained by each of the first 10 PCs. o, Expression variation at the two expression layers across mammalian organs for downsampled data. For this analysis data were downsampled to 2.5 million reads in each library. See Fig. 1d for the analysis of the full dataset. Organ and species icons are from a previous study²⁵.