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DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability

ABSTRACT: DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability

OTHER RELATED OMICS DATASETS IN: GSE99517

PROVIDER: PRJNA388686 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5634090.fastq.gz	Fastqsanger.gz
	SRR5634100.fastq.gz	Fastqsanger.gz
	SRR5634110.fastq.gz	Fastqsanger.gz
	SRR5634120.fastq.gz	Fastqsanger.gz
	SRR5634130.fastq.gz	Fastqsanger.gz

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DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability

Project description:We present DRUID (for Determination of Rates Using Intron Dynamics), a computational pipeline, for determining mRNA stability transcriptome-wide uses metabolic labeling and approach-to-equilibrium kinetics. Our pipeline uses endogenous introns to normalize time course data and yields more reproducible half-lives than other methods, even with datasets that were otherwise unusable. DRUID can handle datasets from a variety of organisms, spanning yeast to humans.

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DRUID: a pipeline for transcriptome-wide measurements of mRNA stability.

Project description:Control of messenger RNA (mRNA) stability is an important aspect of gene regulation. The gold standard for measuring mRNA stability transcriptome-wide uses metabolic labeling, biochemical isolation of labeled RNA populations, and high-throughput sequencing. However, difficult normalization procedures have inhibited widespread adoption of this approach. Here, we present DRUID (for determination of rates using intron dynamics), a new computational pipeline that is robust, easy to use, and freely available. Our pipeline uses endogenous introns to normalize time course data and yields reproducible half-lives, even with data sets that were otherwise unusable. DRUID can handle data sets from a variety of organisms, spanning yeast to humans, and we even applied it retroactively on published data sets. We anticipate that DRUID will allow broad application of metabolic labeling for studies of transcript stability.

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