Reid et al. 2015 (PRJNA281481)

General Details

Title Methods comparison for ribosome profiling
Organism
Number of Samples 2
Release Date 2015/04/17 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP057384
ENA SRP057384
GEO GSE68008
BioProject PRJNA281481

Publication

Title
Authors Reid DW, Shenolikar S, Nicchitta CV
Journal Methods (San Diego, Calif.)
Publication Date 2015 Dec
Abstract The development and application of ribosome profiling has markedly advanced our understanding of ribosomes and mRNA translation. The experimental approach, which relies on deep sequencing of ribosome-protected mRNA fragments generated by treatment of polyribosomes with exogenous nucleases, provides a transcriptome-wide assessment of translation. The broad application of ribosome profiling has been slowed by the complexity and expense of the protocol. Here, we provide a simplified ribosome profiling method that uses micrococcal nuclease to generate ribosome footprints in crude cellular extracts, which are then purified simply by size selection via polyacrylamide gel electrophoresis. This simplification removes the laborious or expensive purification of ribosomes that has typically been used. This direct extraction method generates gene-level ribosome profiling data that are similar to a method that includes ribosome purification. This protocol should significantly ease the barrier to entry for research groups interested in employing ribosome profiling. Copyright © 2015 Elsevier Inc. All rights reserved.
PMC PMC4684803
PMID 26164698
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1979671 PRJNA281481 Homo sapiens Lymphocytes Ribo-Seq 0.0
SRR1979672 PRJNA281481 Homo sapiens Lymphocytes Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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