Extended Data Fig. 3: Optimization of ribosome footprinting method.

a, LUC induction after ETI activation. WT and hem1 plants carry the isogenic Dex:AvrRpt2 cassette. Data are mean ± s.d. of the absolute LUC grey value post ETI induction by Dex treatment (n = 24). b, Polysome profiling of WT and hem1 without (Mock) or with ETI induction (Dex). c, Cutting preference of RNase T1 compared to RNase I. Nucleotides of 3' read ends were counted. Mean ± s.d. (n = 4). d, Mapping ratio of RF read to nuclear protein-encoding genes using RNase T1 in this study and RNase I (Hsu et al., 2017). Mean ± s.d. (n = 4). Two-sided Student’s t-test. e, Read distribution of RS (upper) and RF (bottom) around start (left) and stop codons (right) using 5' read ends. f, Correlation between two replicates (Rep1/2) of RNA-seq (RS) and Ribo-seq (RF) samples of WT and hem1. Data are shown as the correlation of log₂RPKM in CDS for expressed genes with RPKM in CDS ≥ 1. r, Pearson correlation coefficient tested by two-sided Student’s t-test. g, Formulations of the transcriptome (RSfc), translatome (RFfc) and translation efficiency (TEfc) changes from the previous state (denominator) to the current state (numerator). Statistical methods used to describe the significance of each change are parenthesized.