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>Blevins_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>Blevins_Tavella_geneswithdifferentialexpression.xlsx: list of genes that follow different kinds of regulation (homodirectional, compensated mRNA change, translational regulation) as well as genes with increased or decrease translational efficiency (TE) during stress according to Ribodiff.<br>