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

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, transcripts that did not overlap with annotated genes were kept and combined with the gene annotations.<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>Tavella_etal_X_up.csv: list of genes significantly up-regulated by Ribo-Seq (X=RP) or RNA-Seq (X=RNA).<br>Tavella_etal_X_down.csv: list of genes significantly down-regulated by Ribo-Seq (X=RP) or RNA-Seq (X=RNA).Scerevisiaes_5UTR.gtf: annotation file for the 5'UTRs of <i>S.cerevisiae</i> S288C.<br>gene_lists: quantitative RNA (RNA-Seq and Ribo-Seq) and protein (mass spec) data for all genes analyzed; list of genes from Figure 6.<br>

Tavella_etal_Scer_transcriptome.gtf：酿酒酵母（S.cerevisiae）S288C品系的转录组数据集，包含注释特征的基因组坐标，以及为本品系组装得到的从头（de novo）转录本。本研究对在正常及氧化应激（过氧化氢，H₂O₂）条件下培养的酵母的聚腺苷酸化RNA（polyA+ RNA）进行了RNA测序（RNA-Seq），生成了链特异性双端测序读段。随后使用Trinity软件组装转录组，保留未与已注释基因重叠的转录本，并将其与基因注释结果进行合并。
Tavella_etal_tableofcounts.txt：包含对照组与氧化应激处理组中，核糖体测序（Ribo-Seq，RF）与RNA测序（RNA-Seq，RNA）实验下每个基因的比对读段数量，其中Rep1代表测序重复1，Rep2代表测序重复2。
Tavella_etal_X_up.csv：列出了经核糖体测序（X=RP）或RNA测序（X=RNA）筛选得到的显著上调基因。
Tavella_etal_X_down.csv：列出了经核糖体测序（X=RP）或RNA测序（X=RNA）筛选得到的显著下调基因。
Scerevisiaes_5UTR.gtf：酿酒酵母（S.cerevisiae）S288C品系的5'非翻译区（5'UTR）注释文件。
gene_lists：包含所有分析基因的定量RNA（RNA测序与核糖体测序）及蛋白质（质谱，mass spec）数据，以及图6对应的基因列表。