Ribosome footprinting datasets

Ribosome footprinting datasets for yeast were retrieved from the NCBI GEO database (30) (https://www.ncbi.nlm.nih.gov/geo/) using the search term ((‘Saccharomyces cerevisiae’[ORGN]) AND (‘high throughput sequencing’[Platform Technology Type]) AND ribosome). Returned results were manually screened for such datasets that reported footprinting data, or corresponding footprinting and RNA-Seq data, for standard laboratory yeast strains grown in YPD or SC at 30°C, either formatted as counts per gene, counts per codon, or RPKM. All datasets were reformatted to counts per gene before further computational processing, based on gene length information for the R64-2-1 release of the yeast genome. Datasets for HEK293 cells were identified using a similar strategy but replacing the organism specification in the search term with ‘HEK293’.