Transcriptomics

Dataset Information

298

A comparison of the effects of duplex-specific nuclease, antisense oligonucleotides, and riboZero rRNA depletion on ribo-Seq data from mouse


ABSTRACT: Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. A key step is the depletion of ribosomal RNA that allows sufficient depth of sequencing of the mRNA undergoing ribosomal translation. These data are designed to compare four strategies for ribosomal depletion; a novel strategy based on duplex-specific nuclease using either one or two cycles, the antisense oligonucleotides described in Ingola et al (2012) and the commercially available RiboZero kit (with a no treatment control).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus  

SUBMITTER: Ian Brierley   Nerea Irigoyen   Andrew E Firth   Thomas James Hardcastle  

PROVIDER: E-MTAB-3583 | ArrayExpress | 2015-10-16

SECONDARY ACCESSION(S): ERP010521

REPOSITORIES: ArrayExpress, ENA

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Publications

The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.

Chung Betty Y BY   Hardcastle Thomas J TJ   Jones Joshua D JD   Irigoyen Nerea N   Firth Andrew E AE   Baulcombe David C DC   Brierley Ian I  

RNA (New York, N.Y.) 20150818 10


Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient,  ...[more]

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