Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Methods comparison for ribosome profiling

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE68008 | GEO | 2015/07/01

SECONDARY ACCESSION(S): PRJNA281481

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

2013-10-17 | GSE48933 | GEO

Ribosome profiling of Streptomyces griseus NBRC13350 and Streptomyces venezuelae ATCC15439

Project description:We performed ribosome profiling which is the deep-sequencing of mRNA fragments protected by translating ribosome for two Streptomyces species through different growth phases to provide the translatome data

2020-03-03 | GSE138278 | GEO

Ribosome profiling of MCF10A cells with tRNA-Tyr-GUA depletion by shRNA relative to shControl cells

Project description:We report the changes in ribosome protected fragments as measured by ribosome profiling in cells with or without depletion of tRNA-Tyr-GUA

2019-09-25 | GSE120383 | 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 51-base length single read ribosome profiling data on human fibroblasts and cybrid cells using an adapted ribosome profiling protocol; and 51-base length single read RNAseq on polyA enriched RNA

2013-10-17 | E-GEOD-48933 | biostudies-arrayexpress

Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling

Project description:Experiments for optimization of the ribosome profiling protocol using C. elegans lysates. We report that optimizing the cutting accuracy to a narrow window of 28-30 nucleotides when PAGE-purifying the ribosome-protected fragments (RPFs) significantly improves the quality of the RPF library. In addition, we find that purifying monosomes by sucrose gradient fractionation clearly removed more contaminating ribosomal RNA from the samples compared to the purification by gel filtration columns.

2018-02-12 | GSE65948 | GEO

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

Ribosome Footprinting (RiboSeq) analysis of mRNA translation in Dis3l2 knockout mESCs

Project description:Input mRNAs and ribosome protected fragments (RPFs) from Heterozygout (Control) and Dis3l2 knockout (KO) mESCs cultures were analyzed by TruSeq Ribo Profile (Illumina) library preparation and high throughput sequencing

2020-04-04 | GSE136350 | GEO

Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_2]

Project description:Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. These distinct ribosome conformational states revealed by ribosome profiling are seen in all eukaryotes tested including fungi, worms and mammals. This high-resolution ribosome profiling approach reveals the anticipated Rck2-dependent inhibition of translocation through eEF2 phosphorylation during hyperosmotic stress. These same approaches reveal a strong translation elongation arrest during oxidative stress where the ribosomes are trapped in a pre-translocation state, but in this case the translational arrest is independent of Rck2-driven eEF2 phosphorylation. These results provide new insights and approaches for defining the molecular events that impact translation elongation throughout biology.

2019-01-27 | GSE115159 | GEO

Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_1]

2019-01-27 | GSE115158 | GEO