Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome A

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Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA).

Bioinformatics. 2012 Jan 28;

Authors: Schwalb B, Schulz D, Sun M, Zacher B, Dümcke S, Martin D, Cramer P, Tresch A

Abstract
SUMMARY: 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 these 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. AVAILABILITY: DTA is part of R/Bioconductor. To download and install DTA refer to http://bioconductor.org/packages/2.1.../html/DTA.html. CONTACT: schwalb@lmb.uni-muenchen.de.


PMID: 22285829 [PubMed - as supplied by publisher]



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