Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosome Profiling with CNOT1 depletion

ABSTRACT: Ribosome profiling in HEK293 cells with and without the depletion of CNOT1. This allows the determination of translational efficiency and nucleotide resolution of ribosome occupancy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE158141 | GEO | 2021/08/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Ribosome Profiling with CNOT1 depletion

Project description:Ribosome Profiling with CNOT1 depletion

| PRJNA664116 | ENA

mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

Project description:Determination of mRNA half-life in HEK293 cells with and without the depletion of CNOT1.

2021-08-22 | GSE158619 | GEO

RNA-seq of ER-targeted and cytosolic mRNAs with control or CNOT1-targeting siRNA treatment in HEK293 cells

Project description:Determination of mRNA localisation in HEK293 cells with and without the depletion of CNOT1

2021-09-07 | GSE183148 | GEO

A global overview of translation efficiency and ribosome occupancy at nucleotide resolution in HEK293 cells

Project description:Looking at ribosome distribution and translational efficiency in control conditions in HEK293 cell line. Combining this information with our other datasets from HEK293 cells has allowed us to look at ribosome occupancy of specific groups of mRNAs

2019-10-09 | GSE134517 | GEO

A global overview of translation efficiency and ribosome occupancy at nucleotide resolution in HEK293 cells

Project description:A global overview of translation efficiency and ribosome occupancy at nucleotide resolution in HEK293 cells

| PRJNA556704 | ENA

CNOT1 and Transcriptomic Landscape of a HeLa Cell Line

Project description:Purpose: The goals of this study are to compare NGS-derived total transcriptome profiling (RNA-seq) of CNOT1-depleted cells (using siRNA) with control HeLa cells before and after DNA damage to examine quantitative gene expression.

2019-12-05 | GSE141496 | GEO

Analysis of mitochondrial gene expression with Ribosome Profiling

Project description:Ribosome profiling (RiboSeq) maps positions of translating ribosomes on the transcriptome. Here we optimized ribosome profiling for footprinting mitochondrial ribosomes, and profiled three human cell-lines - HEK293, a PDE12-/- knockout, and a deltaFLP 143B cybrid.

2017-07-25 | E-MTAB-5519 | biostudies-arrayexpress

Nuclease-mediated depletion biases in ribosome footprint profiling libraries

Project description:Ribosome footprint profiling is a high throughput sequencing based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally abundant, ribosomal RNA sequences in order to save on sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.

2020-03-27 | GSE147324 | GEO

mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

Project description:mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

| PRJNA665988 | ENA

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

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