Ribosome profiling data and matched mRNA-seq data from HeLa cells corresponding to the experiments (mock transfected 12 hr time point) presented in Guo et al. [22] were downloaded from the NCBI GEO (GSE22004). The expression level of the filtered set of lincRNAs and of RefSeq NM transcripts was evaluated as above. The 803 lincRNAs expressed at an FPKM>1 and a sample of 1292 RefSeq NM transcripts expressed at an FPKM>1 (divided into their constituent CDS and 3′ UTR regions) were broken up into 30 bp windows with a 1 bp offset. A modified version of HTSeq (described above) was used to count reads aligning to each window for both RNA-seq and ribosomal profiling data. The ratio of ribosome-associated reads over mRNA-seq reads was evaluated for each window and the maximum ratio for a given transcript was taken as a measure of ribosome engagement. The whiskers of the box and whisker plot in Figure 2B extend to +/−1.5 times the interquartile range with outliers depicted as dots. Wilcoxon rank sum test was used to calculate P values.
