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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
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 of Mycobacterium tuberculosis under nutrient starvation
We have performed parallel ribosome profiling and RNA sequencing to determine which mRNAs are being translated during exponential growth and following 24 hours of nutrient starvation in the human pathogen Mycobacterium tuberculosis.
ORGANISM(S): Mycobacterium tuberculosis H37Rv 
2021-02-02 | E-MTAB-8835 | 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
TranscriptomicsRibosome profiling with MN and RNaseI
The aim of this experiment is to compare nucleases used in ribosome profiling using Drosophila melanogaster Kc167 cells and human U2OS osteosarcoma cells. Ribosome profiling was performed from nuclease digested samples using sucrose cushion centrifugation separated ribosomes.
ORGANISM(S): Homo sapiens 
2015-01-08 | E-MTAB-2421 | biostudies-arrayexpress
TranscriptomicsTranslational control through ribosome traffic jams and aborted protein synthesis
Translational control is a widespread mode of gene regulation in organisms ranging from bacteria to mammals. Computational models posit that translational control of protein expression during elongation is exerted through a traffic jam of multiple ribosomes at ribosome pause sites on mRNAs. Yet neit...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-05-15 | E-GEOD-51052 | biostudies-arrayexpress
TranscriptomicsClarifying the translational pausing landscape in bacteria by ribosome profiling
The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausi...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2016-01-13 | E-GEOD-72899 | biostudies-arrayexpress
TranscriptomicsAdvancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping
Since the initial publication of the trypanosomatid genomes, curation has been ongoing. Here we apply the technique of ribosome profiling to Trypanosoma brucei, identifying 223 new coding regions by virtue of ribosome occupancy in the corresponding transcripts. A small number of these putative genes...
ORGANISM(S): Trypanosoma brucei 
2015-12-22 | E-GEOD-72463 | biostudies-arrayexpress
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