E-MTAB-2934 - Examples of ribosome profiling in chlamydomonas and mouse

Status
Last updated on 16 October 2015, released on 16 October 2015
Organism
Chlamydomonas reinhardtii, Mus musculus
Samples (4)
Protocols (10)
Description
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 employs duplex-specific nuclease as a convenient, bias-free, species-independent way to reduce rRNA contamination. Our protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream and overlapping open reading frames (ORFs). This feature also allows the identification of an alternative ribosome conformation evident during termination of protein synthesis. To test the effectiveness of DSN in ribosome profiling, we generated Ribo-Seq libraries from mouse tissue culture cells and from the green alga Chlamydomonas reinhardtii.
Experiment types
other, optimization design
Contacts
Citation
The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis. Chung BY, Hardcastle TJ, Jones JD, Irigoyen N, Firth AE, Baulcombe DC, Brierley I.  (2015), PMID:26286745
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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