Associated data from: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae

This dataset includes two custom BED files described in "An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae" (Ridenour and Donczew, submitted), which were used to define counting windows for processing SLAM-seq data in SLAM-DUNK (version 0.4.3) [1]. The BED files contain all annotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome or the Schizosaccharomyces pombe genome and were created using BEDOPS (version 2.4.3) [2]. All ORFs were then extended 250 bp beyond their stop position to capture 3′ untranslated regions (UTRs) using SAMtools (version 1.14) [3] and BEDTools (version 2.30.0) [4]. The reference genome annotations for S. cerevisiae strain S288C (version R64-3-1, RefSeq Assembly GCF_000146045.2) and S. pombe strain 972h- (version ASM294v2, RefSeq Assembly GCF_000002945.1) were retrieved from the NCBI Datasets repository. The S. cerevisiae chromosome names were modified to reflect standard nomenclature (https://www.yeastgenome.org/).本数据集包含两篇自定义BED格式文件（BED），相关描述见于《An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae》（作者Ridenour与Donczew，已投稿）。上述文件用于在SLAM-DUNK（版本0.4.3）中定义处理SLAM-seq数据（SLAM-seq）的计数窗口[1]。该BED格式文件涵盖酿酒酵母（Saccharomyces cerevisiae）基因组或粟酒裂殖酵母（Schizosaccharomyces pombe）基因组中所有已注释的开放阅读框（open reading frames, ORFs），并通过BEDOPS（版本2.4.3）生成[2]。随后，借助SAMtools（版本1.14）[3]与BEDTools（版本2.30.0）[4]，将所有开放阅读框在其终止位置下游延伸250 bp，以捕获3′非翻译区（3′ untranslated regions, UTRs）。酿酒酵母S288C菌株（版本R64-3-1，RefSeq组装编号GCF_000146045.2）与粟酒裂殖酵母972h-菌株（版本ASM294v2，RefSeq组装编号GCF_000002945.1）的参考基因组注释信息均从NCBI Datasets数据库获取。酿酒酵母的染色体名称已按照标准命名规则进行修正（https://www.yeastgenome.org/）。