Extended Data Fig. 2: Quality control metrics for omics data.

a) Proteomics multiplexing design using TMT11 reagents for isobaric tagging and a pooled reference sample. The diagram describes processing of a single tissue. Following multiplexing, peptides were used for protein abundance analysis, serial PTM enriched for phosphosite and optional acetylsite quantification, or ubiquitylsite quantification through enrichment of lysine-diglycine ubiquitin remnants. b) Total number of fully quantified proteins per plex in each global proteome dataset. c-e) The total number of fully quantified phosphosites (c), acetylsites (d), and ubiquitylsites (e) per plex in each dataset. f) Distributions of coefficients of variation (CVs) calculated from metabolomics features identified in pooled samples and analyzed periodically throughout liquid chromatography-mass spectrometry runs. CVs were aggregated and plotted separately for named and unnamed metabolites. g) Transcription start site (TSS) enrichment (top) and fraction of reads in peaks (FRiP, bottom) across ATAC-seq samples per tissue. h) Distributions of RNA integrity numbers (RIN, top) and median 5′ to 3′ bias (bottom) across samples in each tissue in the RNA-Seq data. i) Percent methylation of CpG, CHG and CHH sites in the RRBS data. For boxplots in (h,i): center line represents median; box bounds represent 25th and 75th percentiles; whiskers represent minimum and maximum excluding outliers; filled dots represent outliers. j) Number of wells across multiplexed immunoassays with fewer than 20 beads. Measurements from these 182 wells were excluded from downstream analysis. k) 2D density plot of targeted analytes’ mean fluorescence intensity (MFI) versus corresponding CHEX4 MFI from the same well for each multiplexed immunoassay measurement, where CHEX4 is a measure of non-specific binding.