Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Ribosome profiling (Ribo-seq)

PROVIDER: PRJNA899535 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22234333_1.fastq.gz	Fastqsanger.gz
	SRR22234333_2.fastq.gz	Fastqsanger.gz
	SRR22234334_1.fastq.gz	Fastqsanger.gz
	SRR22234334_2.fastq.gz	Fastqsanger.gz
	SRR22234335_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Ribosome profiling and transcriptome profiling of MCF-7 cells

Project description:We performed ribosome profiling (RIBO-seq) and transcriptome profiling (RNA-seq) to monitor RNAs associated with ribosome in the MCF-7 cell model Keywords: ribosome profiling, translation, MCF-7

2018-07-13 | GSE111866 | GEO

Detection of SEPs by MS - Unraveling the hidden universe of small proteins in bacterial genomes

Project description:Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is not feasible. Herein we have used MS to characterize smORFomes of different Mycoplasma species. This data is used to corroborate the predictions of a random forest classifier that in silico predicts all the putative SEPs encoded by different bacterial genomes.

2019-03-01 | PXD008243 | Pride

Detection of SEPs by MS (Second Round)

Project description:Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is not feasible. Herein we have used MS to characterize smORFomes of different Mycoplasma species and Escherichia coli. This data is used to corroborate the predictions of a random forest classifier that in silico predicts all the putative SEPs encoded by different bacterial genomes.

2019-10-14 | PXD010490 | Pride

A spectral analysis approach to detects actively translated open reading frames in high resolution ribosome profiling data

Project description:RNA sequencing protocols allow for quantifying gene expression regulation at each individual step, from transcription to protein synthesis. Ribosome Profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. Despite its great potential, a rigorous statistical approach to identify translated regions from Ribo-seq data is not yet available. To fill this gap, we developed RiboTaper, which quantifies the significance of the three-nucleotide periodicity of Ribo-seq reads via spectral analysis methods. Examination of RNA fragments protected by ribosome

2015-11-12 | E-GEOD-73136 | biostudies-arrayexpress

Detection of SEPs by MS (Second Round)

Project description:Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is not feasible. Herein we have used MS to characterize smORFomes of different Mycoplasma species, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa. This data is used to corroborate the predictions of a random forest classifier that in silico predicts all the putative SEPs encoded by different bacterial genomes.

2019-10-14 | PXD011038 | Pride

Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

Project description:In the ribosome complex, tRNA is a critical element of mRNA translation. We reported a new technology for profiling ribosome-embedded tRNAs and their modifications. With the method, we generated a comprehensive survey of the quanity and quality of intra-ribosomal tRNAs (Ribo-tRNA-seq). Ribo-tRNA-seq can provide new insights on translation control mechanism in diverse biological contexts.

2018-03-19 | E-MTAB-6576 | biostudies-arrayexpress

Ribosome profiling of HEK293 cells.

Project description:The development of the ribosome profiling (ribo-seq) technique has enabled the measurement of translation at a genome-wide level. There are several variants of the ribosome profiling technique that use different translation inhibitors. The regular ribo-seq utilizes Cycloheximide (CHX), a translation elongation inhibitor to freeze all translating ribosomes. In contrast to CHX, the translation inhibitor lactimidomycin (LTM) and harringtonine (Harr) have a much stronger effect on initiating ribosomes. The use of these inhibitors allows for the global mapping of translating initiating sites (TISs) when they are coupled with ribosome profiling (TI-seq). We have developed a computational tool to detect and/or quantitatively compare translation initiation from TI-seq data, and predict novel ORFs from regular CHX-based ribo-seq data. Two replicates of CHX-based ribo-seq experiments and one Harr based ribo-seq were performed in HEK293 cells for confirming the ORFs predicted using public available data.

2018-01-22 | GSE94460 | GEO

mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition

Project description:mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition mRNA-seq and Ribo-seq

2013-06-21 | E-GEOD-48140 | biostudies-arrayexpress

Ribosome profiling and RNA sequencing of ED fibroblast cells in response to infection by equine torovirus, Berne strain.

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of equine torovirus.

2018-05-15 | E-MTAB-6656 | biostudies-arrayexpress

Ribo-seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation to determine effects on translation.

2021-09-30 | E-MTAB-9094 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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