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/).