Ribosome speed - OmicsDI

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1 The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark 2 Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark 4 Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark (1)
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Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, Australia (1)

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Ribosome 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

Distinct 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

Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells

In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positi...

ORGANISM(S): Homo sapiens

2016-02-09 | E-GEOD-46613 | biostudies-arrayexpress

Cell 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

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data

Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Existing approaches make use of sequence fragment length or frame occupancy to differentiate between active translation and background noise, however they do not consider additional characteristic...

ORGANISM(S): Homo sapiens

2016-07-01 | E-GEOD-75947 | biostudies-arrayexpress

Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed

PRJNA1294329 | ENA

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5′–3′ transcript degradation follows the last translating ribosome, producing...

ORGANISM(S): Schizosaccharomyces pombe

2015-06-04 | E-GEOD-63120 | biostudies-arrayexpress

Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells

The transcription factor RUNX1 is frequently mutated in myelodysplastic syndrome and leukemia. RUNX1 mutations can be early events, creating pre-leukemic stem cells that expand in the bone marrow. Here we show that, counter-intuitively, Runx1 deficient hematopoietic stem and progenitor cells (HSPCs)...

ORGANISM(S): Mus musculus

2015-07-27 | E-GEOD-67609 | biostudies-arrayexpress

Ribosome profiling of UNR (CSDE1) KD

Investigation of the effects of UNR (CSDE1) knock-down on translation in Melanoma Cells using Ribosome Profiling

ORGANISM(S): Homo sapiens

2016-11-07 | E-MTAB-3815 | biostudies-arrayexpress

Transcription profiling of wild type, dcgrA knock out and reconstituted wild type Aspergillus fumigatus to determine the contribution of CgrA to ribosome biogenesis

Study to determine the contribution of CgrA to ribosome biogenesis in Aspergillus fumigatus.

ORGANISM(S): Aspergillus fumigatus

2008-01-03 | E-MEXP-1324 | biostudies-arrayexpress

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