title: Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA).
abstract: Standard transcriptomics measures total cellular RNA levels. Our understanding of gene regulation would be greatly improved if we could measure RNA synthesis and decay rates on a genome-wide level. To that end, the Dynamic Transcriptome Analysis (DTA) method has been developed. DTA combines metabolic RNA labeling with standard transcriptomics to measure RNA synthesis and decay rates in a precise and non-perturbing manner. Here, we present the open source R/Bioconductor software package DTA. It implements all required bioinformatics steps that allow the accurate absolute quantification and comparison of RNA turnover.
authors.affiliation: Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany. schwalb@lmb.uni-muenchen.de
authors.forename: Björn
authors.initials: B
authors.lastname: Schwalb
authors.forename: Daniel
authors.initials: D
authors.lastname: Schulz
authors.forename: Mai
authors.initials: M
authors.lastname: Sun
authors.forename: Benedikt
authors.initials: B
authors.lastname: Zacher
authors.forename: Sebastian
authors.initials: S
authors.lastname: Dümcke
authors.forename: Dietmar E
authors.initials: DE
authors.lastname: Martin
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
mesh_terms: D002453:Cell Cycle; D020869:Gene Expression Profiling / Q000379:methods*; D055106:Genome-Wide Association Study; D020411:Oligonucleotide Array Sequence Analysis; D020871:RNA Stability; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics; D012568:Schizosaccharomyces / Q000166:cytology / Q000235:genetics; D012984:Software; D059467:Transcriptome