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TranscriptomicsRibosome hibernation factor promotes Staphyloccocal survival and differentially represses translation
We sequenced a total of 16 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from S. aureus hpf mutant (NE838) and its parental strain JE2 grown in tryptic soy broth (TSB) or minimal medium (MM). The data represented 2 independent biological replicates. Examination of t...
ORGANISM(S): Staphylococcus aureus 
2016-03-29 | E-GEOD-74197 | biostudies-arrayexpress
TranscriptomicsThe ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome pr...
ORGANISM(S): Homo sapiens 
2012-07-26 | E-GEOD-37744 | biostudies-arrayexpress
TranscriptomicsRibosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes
The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep-sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a p...
ORGANISM(S): Mus musculus 
2011-11-03 | E-GEOD-30839 | biostudies-arrayexpress
TranscriptomicsCell type-specific ribosome profiling in vivo.
We report cell-type specific ribosome profiling in a mouse glioma model. We report a strategy for cell-type specific ribosome profiling in vivo. Our strategy was applied to the characterization of a mouse glioma model.
ORGANISM(S): Mus musculus 
2014-08-25 | E-GEOD-51424 | biostudies-arrayexpress
TranscriptomicsRibosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration
In higher eukaryotes, the large numbers of nuclear-encoded tRNA genes partially ensure the robustness of cytoplasmic protein translation. Here we discover that a loss-of-function in n-Tr20, a member of the nuclear-encoded tRNA Arg UCU family that is expressed specifically in the central nervous syst...
ORGANISM(S): Mus musculus 
2014-07-28 | E-GEOD-56127 | biostudies-arrayexpress
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
ProteomicsRibosome quality control activity potentiates vaccinia virus protein synthesis during infection
Ribosomes are highly abundant cellular machines that perform the essential task of translating the genetic code into proteins. Cellular translation activity is finely tuned and proteostasis insults, such as those incurred upon viral infection, activate stress signaling pathways that result in transl...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Vaccinia Virus Wr (ncbitaxon:10254) 
2021-01-05 | MSV000086660 | MassIVE
TranscriptomicsRibosome profiling data obtained from HEK293T cells 30 minutes after treatment with arsenite to a final concentration of 40 M-BM-5M
Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eIF2. However, the persistent translation of certain mRNAs is required for deployment of an adequate s...
ORGANISM(S): Homo sapiens 
2015-01-27 | E-GEOD-55195 | biostudies-arrayexpress
TranscriptomicsTime resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells
Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess earl...
ORGANISM(S): Rattus norvegicus 
2015-04-10 | E-GEOD-60752 | biostudies-arrayexpress
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
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