Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE134517 | GEO | 2019/10/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

Ribosome Profiling with CNOT1 depletion

Project description: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.

2021-08-23 | GSE158141 | 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

Monosome profiling in starved HEK293 cells

Project description:Ribosome profiling from monosome and polysome fractions of serum or amino acid starved HEK293 cells

2022-08-04 | GSE129912 | GEO

Analysis of ribosomal occupancy with ribosome profiling.

Project description:Ribosome profiling was prepared in parallel with RNA-seq, using the same protocol for cDNA library preparation.

2015-03-01 | E-MTAB-2941 | biostudies-arrayexpress

Genome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Project description:Techniques for systematically monitoring protein translation have lagged far behind methods for measuring mRNA levels. Here we present a ribosome profiling strategy, based on deep sequencing of ribosome protected mRNA fragments, that enables genome-wide investigation of translation with sub-codon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control both for determining absolute protein abundance and for responding to environmental stress. We also observed distinct phases during translation involving a large decrease in ribosome density going from early to late peptide elongation as well as wide-spread, regulated initiation at non-AUG codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible. Examine replicates of ribosome footprints and mRNA abundance in biological replicates of log-phase growth and acute amino acid starvation

2009-02-12 | E-GEOD-13750 | biostudies-arrayexpress

Starved HEK293 cells

Project description:Starved HEK293 cells

| PRJNA533129 | ENA

Analysis of ribosomal occupancy with ribosome profiling.

Project description:Analysis of ribosomal occupancy with ribosome profiling.

| PRJEB7282 | ENA

RNA-seq of HEK293-TRDMT1-KD and HEK293 control

Project description:RNA-seq of HEK293-TRDMT1-KD and HEK293 control

| PRJNA558168 | ENA