Lauria et al. 2018 (PRJNA438445)

General Details

Title Ribosome profiling and transcriptome profiling of MCF-7 cells
Organism
Number of Samples 1
Release Date 2018/03/15 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP135757
ENA SRP135757
GEO GSE111866
BioProject PRJNA438445

Publication

Title
Authors Lauria F, Tebaldi T, Bernabò P, Groen EJN, Gillingwater TH, Viero G
Journal PLoS computational biology
Publication Date 2018 Aug
Abstract Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine the trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies. riboWaltz was implemented in R and is available as an R package at https://github.com/LabTranslationalArchitectomics/RiboWaltz.
PMC PMC6112680
PMID 30102689
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6838651 PRJNA438445 Homo sapiens MCF7 Ribo-Seq Cycloheximide
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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