Extended Data Fig. 7: Quality control and analysis of single-organoid ribo-seq analysis.
From: A programmed decline in ribosome levels governs human early neurodevelopment
a The ribo-seq data exhibit high start site coverage across samples based upon metagene analysis of CDS regions. b. The ribo-seq data exhibit high stop site coverage across samples based upon metagene analysis of CDS regions. c. Violin/scatter dot plot quantifying TE changes relative to predicted 5’UTR free energy normalized to UTR length. ****P < 0.0001. Dunnett’s T3 multiple comparisons test(two-sided). n = 7982 (total), 37 (FDR < 0.1), 140 (FDR < 0.2) transcripts, P = 6.016844e-07(total vs FDR < 0.1), P = 2.003477e-19(total vs FDR < 0.2). d. Box dot plot quantifying TE changes relative to log2 transformed 5’UTR length. ****P < 0.0001. Dunnett’s T3 multiple comparisons test(two-sided). n = 7982 (total), 37 (FDR < 0.1), 140 (FDR < 0.2) transcripts, P = 9.487886e-11(total vs FDR < 0.1), P = 2.29069e-15 (total vs FDR < 0.2). In the order of groups “total transcript”, “FDR < 0.1”, “FDR < 0.2”, Minimum=1.58, 4.64, 1.58, Maximum=11.1, 8.03, 8.76, median=7.12, 5.75, 5.99, Q1(25%, lower bound)=6.11, 5.25, 5.29, Q3(75%, upper bound)=7.98, 6.23, 6.69, lower whisker=3.30, 4.64, 3.18, upper whisker=10.79, 7.70, 8.77,. e. Example of TOP-like element containing transcripts identified in this study. f. Motifs enriched in the 5’UTRs of AIRIMV190G sensitive transcripts are shown. P values were calculated based on the hypergeometric distribution (two-sided, multiple-comparison corrected test).
