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TranscriptomicsDistinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA...
ORGANISM(S): Saccharomyces cerevisiae 
2014-06-10 | E-GEOD-58321 | biostudies-arrayexpress
TranscriptomicsTime-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics
Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomi...
ORGANISM(S): Homo sapiens 
2017-05-18 | E-GEOD-69047 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
DEAD-box RNA helicases eIF4A and Ded1 are believed to promote translation initiation by resolving mRNA secondary structures that impede ribosome attachment at the mRNA 5’ end or subsequent scanning of the 5’UTR, but whether they perform distinct functions or act redundantly in vivo is poorly underst...
ORGANISM(S): Saccharomyces cerevisiae 
2015-03-02 | E-GEOD-66411 | biostudies-arrayexpress
TranscriptomicsGenome-wide translational analysis of RAW264 macrophages by ribosome profiling
Purpose: The aim is to analyze the translational kinetics of the basal and LPS-stimulated conditions of RAW264 macrophages focusing on ribosome density Method: RAW264 macrophages were cultured at 3.0 x 10^5 cells/ml in media (DMEM, 2mM Glutamine, 10% FBS, 100 units penicillin and 100µg streptomycin...
ORGANISM(S): Mus musculus 
2015-11-01 | E-GEOD-60930 | biostudies-arrayexpress
TranscriptomicsCausal signals between codon bias, mRNA structure and the efficiency of translation and elongation
Ribosome profiling data reports on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translati...
ORGANISM(S): Saccharomyces cerevisiae 
2015-01-05 | E-GEOD-63789 | biostudies-arrayexpress
ProteomicsH.sapiens - Cell line, Hct116 (Koch,proteomics,2014)
abundance based on MAPPED_BY_AUTHORS, HCT116, Interaction consistency score: 4.6, Coverage: 5
ORGANISM(S): 9606 
2014-00-00 | 1430705385 | PAXDB
GenomicsModeling ribosome dwell times and relationship with tRNA loading and codon usage in mammals (Ribosome Profiling)
Modeling ribosome dwell times and relationship with tRNA loading and codon usage in mammals (Ribosome Profiling)
PRJNA521742 | ENA
UnknownRibosome profiling reveals features of normal and disease-associated mitochondrial translation.
Not available
S-EPMC3863897 | biostudies-literature
TranscriptomicsTranscription profiling of Saccharomyces cerevisiae eIF4G isoforms to investigate eIF4G deletion ribosome occupancy
Effect of eIF4G gene deletion on the ribosome occupancy.
ORGANISM(S): Saccharomyces cerevisiae 
2009-10-24 | E-MEXP-2399 | biostudies-arrayexpress
UnknownTime-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics.
Not available
S-EPMC5546878 | biostudies-literature
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