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TranscriptomicsAbsolute quantification of protein production reveals principles underlying protein synthesis rates
A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resul...
ORGANISM(S): Escherichia coli 
2014-04-24 | E-GEOD-53767 | biostudies-arrayexpress
ProteomicsChanges in Protein Turn-over Rates Regulate Tryptophan and Glucosinolate Biosynthesis, IAA Transport and Photosynthesis in Arabidopsis Growth and Defense Transitions
Changes in protein synthesis and degradation rates, transcript, protein and phytohormone abundance of 99 targets using qPCR and LC-MS parallel reaction monitoring (PRM) were measured in the transitions between optimal growth conditions (homeostasis), fully induced pattern triggered immunity (PTI) an...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-10-13 | PXD041215 | Pride
Translational regulation Photosynthesis Protein degradation rates Pti Glucosinolates Myc2 Phytohormone Proteomics Protein synthesis rates Auxin Pin proteins 
ProteomicsProtein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates
Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we he...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-09-10 | PXD014357 | Pride
Protein charge Yeast Translation Tasep Ribosomal proteins 
GenomicsscDUAL-seq Simultaneously Measures RNA Synthesis and Degradation Rates in Single Cells
scDUAL-seq Simultaneously Measures RNA Synthesis and Degradation Rates in Single Cells
PRJNA1209856 | ENA
ProteomicsIn utero pulse-injection of isotopic amino acids quantifies protein turnover rates during murine fetal development
Protein translational control is a highly regulated step in the gene expression program during development and tools to quantify protein synthesis rates in a developing fetus are lacking. Here, we developed a novel in utero approach to quantify tissue-specific translational kinetics of the nascent p...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2021-04-30 | MSV000087342 | MassIVE
ProteomicsProtein synthesis during myoblast differentiation
Mole (MSR) and fractional (FSR) synthesis rates of proteins during C2C12 myoblast differentiation were investigated. Myoblast cultures supplemented with D2O during 0-24 h or 72-96 h of differentiation were analysed by LC-MS/MS to calculate protein FSR and MSR after samples were spiked with yeast alc...
ORGANISM(S): Mus musculus (Mouse) 
2020-10-22 | PXD021125 | Pride
C2c12  muscle  fractional synthesis rate 
TranscriptomicsMeasurement of temperature affects on Arabidopsis transcription and decay rates
The goal of this study is to measure Arabidopsis mRNA transcription and mRNA decay rates genome wide at two temperatures, and thus to calculate the temperature coefficient of both processes. Sensing and response to ambient temperature is important for controlling growth and development of many organ...
ORGANISM(S): Arabidopsis thaliana 
2013-12-07 | E-GEOD-53071 | biostudies-arrayexpress
ProteomicsDeuterium oxide labeling methods for bulk and single muscle protein synthesis measures, and measures of integrated muscle protein synthesis and breakdown rates
This methodological pilot study explored the feasibility of an integrated tracer approach for simultaneous measurement of human skeletal muscle protein synthesis and breakdown during prolonged deuterium oxide (²H₂O) labelling. Four healthy men completed a five week protocol combining daily oral ²H₂O...
ORGANISM(S): Homo sapiens (Human) 
2026-09-07 | PXD078552 | Pride
Human Skeletal muscle Protein trunover 
ProteomicsA novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor.
We developed a pulse-chase variant of SILAC (stable isotope labeling by amino acids in cell culture pcSILAC). pcSILAC can quantitate in one experiment and for two conditions the relative levels of proteins newly synthesized in a given time as well as the relative levels of remaining preexisting prot...
ORGANISM(S): Homo sapiens (Human) 
2013-12-10 | PXD000538 | Pride
Hsp90 T-cells Pulse-chase Silac Synthesis rate Decay rate 
GenomicseIF5A depletion effect on synthesis and decay rates of yeast genes
eIF5A depletion effect on synthesis and decay rates of yeast genes
PRJNA1290098 | ENA
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