Extended Data Fig. 9: Comparison of 47S O-MAP-Seq and HyPro-Seq.
a, Heatmap of Pearson correlations, comparing three biological replicates of 47S O-MAP-Seq and two biological replicates (four technical replicates each) of the analogous HyPro-Seq experiment. Comparisons were made between log2(fold change, enriched/input) for each replicate. Note the high inter-replicate reproducibility of O-MAP (r = 0.87–0.93), and that its correlation to HyPro-Seq Replicate A (r = 0.53–0.58) is comparable to the correlation between HyPro-Seq biological replicates (r = 0.55–0.56). b, Example scatter plots of the data used in (a), highlighting O-MAP-Seq’s superior reproducibility. c, O-MAP-Seq and HyPro-Seq enrich many of the same transcripts. Volcano plot of 47S O-MAP-Seq data, equivalent to (Fig. 5b), with coding and noncoding isoforms merged. 47S O-MAP-Seq prominently enriches many of the transcripts that were enriched by 47S HyPro-Seq (red), in addition to a smaller set of unique RNAs (blue). Note that relatively few of the transcripts that were uniquely enriched by HyPro-Seq (dark gray) were de-enriched by O-MAP; the majority of these RNAs fell below the significance cutoff of detection, presumably due to the O-MAP-Seq dataset’s lower sequencing depth. Significance testing: Wald’s test. d, Breakdown of 47S-proximal RNAs by transcript class, for those enriched by O-MAP-Seq (blue), HyPro-Seq (gray), and both methods (red). Although the overall composition is similar, HyPro-Seq enriches more protein coding genes and mitochondrial tRNAs, which are not thought to be nucleolar, and fewer lncRNAs and pseudogenic transcripts. e, Isoform-level analysis of enriched transcripts arising from protein-coding genes, analogous to (Fig. 5d). Note that HyPro-Seq enriches a higher proportion of protein-coding isoforms, and lower proportion of retained intron-containing transcripts. Collectively, these data suggest that O-MAP-Seq largely recapitulates the data obtained by analogous methods, but with lower noise and higher reproducibility.
