Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments in HuH-7 cells

ABSTRACT: The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments in HuH-7 cells

PROVIDER: PRJNA527113 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

Project description: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 profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pre-treating cells with harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5 - 7 days to generate a completed ribosome profiling sequencing library. Ribosome profiling in cultured mammalian cells under three different footprinting conditions

2012-07-26 | E-GEOD-37744 | biostudies-arrayexpress

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

2012-07-26 | GSE37744 | GEO

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments in HuH-7 cells

Project description:To globally analyse the lncRNAs with potential coding ability of HCC cells, we performed Ribo-seq using HuH-7 cells. The cycloheximide (CHX) was added to inhibit the translational elongation of ribosomes of the HuH-7 cells.Furthermore,we identified the candidate ORFs with the selected RPF reads using the RiboCode software.

2020-04-30 | GSE128320 | GEO

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

Project description: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 fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle. Ribosome profiling, or sequencing of ribosome-protected mRNA fragments, in yeast. We assay ribosome footprint sizes and positions in three conditions: untreated yeast (3 replicates) and yeast treated with translation inhibitors cycloheximide (2 replicates) and anisomycin (2 biological replicates, one technical replicate). We also treat yeast with 3-aminotriazole to measure the effect of limited histidine tRNAs on ribosome footprint size and distribution (two treatment durations).

2014-06-10 | E-GEOD-58321 | biostudies-arrayexpress

Analysis of Ribosome Protected Fragments of mRNAs from yeast strains either expressing Rio1p or depleted of Rio1p

Project description:mRNAs bound by ribosomes from yeast cells were analysed in order to determine the exact position of ribosomes in the presence or absence of Rio1p. Beside total Ribosome Protected Fragments (RPFs), RPFs from mRNAs protected by immature pre-40S pre-ribosomes was also analysed. The analysis showed that immature 40S ribosomes can carry out translation and their premature entry into translation is hindered by Rio1p.

2017-08-16 | GSE98333 | GEO

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

2014-06-10 | GSE58321 | GEO

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.

Project description: Not available

| S-EPMC3535016 | biostudies-literature

Methods comparison for ribosome profiling

Project description:Assessment of the effecacy of direction extraction of ribosome-protected mRNA fragments for ribosome profiling Immortalized human lymphocytes were analyzed by ribosome profiling protocols with or without ribosome purification

2015-07-01 | E-GEOD-68008 | biostudies-arrayexpress

Methods comparison for ribosome profiling

Project description:Assessment of the effecacy of direction extraction of ribosome-protected mRNA fragments for ribosome profiling

2015-07-01 | GSE68008 | GEO

Ribosome profiling reveals features of normal and disease-associated mitochondrial translation

Project description:Ribosome profiling and RNAseq data on human BJ fibroblasts and cybrid cells using an adapted ribosome profiling protocol to improve detection of mitochondrial ribosome protected fragments

2013-10-17 | GSE48933 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data