Using ribosome profiling to quantify differences in protein expression: a case study in Saccharomyces cerevisiae oxidative stress conditions

Blevins_Tavella_etal_Scer_transcriptome.gtf: Transcriptome of S.cerevisiae that includes the genomic coordinates of annotated features as well as <i>de novo</i> assembled transcripts mapped for <i>S.cerevisiae</i> S288C. We performed RNA-Seq of polyA+ RNA of yeast was grown in normal and oxidative stress conditions (H₂O₂). Paired-end strand-specific sequencing reads were generated. Next, we assembled the transcriptome with Trinity using the sequencing data from all RNA-Seq experiments. Transcripts that did not overlap with annotated genes (XLOC) were kept and combined with the gene annotations to produce the final file.<br><br>Tavella_etal_tableofcounts.txt: Number of mapped reads per gene in Ribo-Seq (RF) and RNA-Seq (RNA) experiments, for control and oxidative stress (treated); Rep1: sequencing replicate 1; Rep2: sequencing replicate 2.<br>Blevins_Tavella_etal_X_up.csv: list of genes significantly up-regulated by Ribo-Seq (X=RP) or RNA-Seq (X=RNA).<br>Blevins_Tavella_etal_X_down.csv: list of genes significantly down-regulated by Ribo-Seq (X=RP) or RNA-Seq (X=RNA).<br>Blevins_Tavella_Scerevisiaes_5UTR.gtf: annotation file for the 5'UTRs of <i>S.cerevisiae</i> S288C.<br>Blevins_Tavella_gene_lists.xlsx: quantitative RNA (RNA-Seq and Ribo-Seq) and protein (mass spec) data for all genes analyzed.<br>