Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Alternative Reading Frame (ARF) overexpression in LN229 glioma cells

ABSTRACT: p14ARF inducible A5 glioma cells express p14ARF after cell exposure to 2 ug of doxycycline

ORGANISM(S): Homo sapiens

SUBMITTER: Abdessamad Zerrouqi

PROVIDER: E-MEXP-3476 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of common human host genes involved in pathogenesis of different rota virus strains-an attempt to recognize probable antiviral targets

Project description:In this study, we aim to identify common human host genes involved in pathogenesis of different rota virus strains as an attempt to recognize probable antiviral targets. We have compared the host gene regulation after infection of human intestinal cell line (HT29) with three different wild type RV strains i.e. SA11 (simian, G3, P2), A5-13 (bovine, G8, P1) and Wa (human, G1, P8). HT29 cells mock infected or infected with three rota virus strains (SA11, A5-13, Wa). At 5hpi total RNA was extracted and microarray was done using Affymetrix protocol.

2013-06-30 | E-MEXP-3670 | biostudies-arrayexpress

Transcription profiling of human U2OS cell line transfected with IZ-1 and 14 ARF expressing plasmids

Project description:U2OS cells were stably transfected with an ecotropic receptor expression plasmid. These cells were infected with retroviruses expressing MIZ-1 or MYC and subsequently superinfected with retroviruses expressing p14ARF. Selection was carried out 48h following superinfection and selected cells were harvested within 1 - 2 passages. For each condition around 2.5x10<superscript6> cells were pooled.<br>Using the two color Quick-Amp labelling kit (Agilent, 5190-0444) 100ng of total RNA were used for cDNA synthesis, aRNA amplification and labelling according to manufacturer's instructions.<br>Transcriptional profiling was done on a whole human genome oligo microarray (Agilent, G4112F, 014850) in a 4x44k slide format.

2009-11-01 | E-MEXP-2310 | biostudies-arrayexpress

Transcription profiling of hind limbs from annexin A5 and A6 knock-out mice

Project description:Initiation of mineralisation during endochondral ossification is a multistep process and was assumed to correlate with specific interactions of annexins and collagens. Annexins A5 and A6 are postulated to represent the essential annexins promoting cartilage mineralisation. However, skeletal development appears to be normal in annexin A5 or A6 deficient mice. The highly conserved structures of annexins led to the assumption that annexins A5 and A6 may fulfill redundant functions. We now generated mice deficient for both proteins, annexins A5 and A6. Mice were viable, fertile and showed no obvious abnormalities. Assessment of skeletal elements using histological, ultrastructural and peripheral quantitative computed tomography methods revealed that mineralisation and development of the skeleton was not significantly affected in mutant mice. In respect of the lack of an obvious phenotype we now applied microarray analysis to the growth plate to define changes in the transcriptome of juvenile murine growth plates from mutant mice. Global gene expression analysis revealed subtle phenotypes at the transcriptome level of genes involved in cell growth and intermediate metabolism in mutant mice. These data demonstrate that both annexins are dispensable for proper cartilage mineralisation but may affect cell proliferation processes at the transcriptomic level.

2009-02-17 | E-MEXP-1718 | biostudies-arrayexpress

Identification of Small Open Reading Frame-Encoded Peptides in Glioma by an Optimized Proteomics Strategy.

Project description: Not available

| S-EPMC12275937 | biostudies-literature

Truncating the i-leader open reading frame enhances release of human adenovirus type 5 in glioma cells.

Project description: Not available

| S-EPMC3090740 | biostudies-literature

Alternative Reading Frame expression in POLG gene

Project description:POLGARF is an upstream Alternative Reading Frame in POLG gene partially overlapping POLG sequence. To obtain POLGARF peptide reference spectra POLGARF was overexpressed in HEK293T and HEK293F cells .

2021-09-08 | PXD016007 | Pride

A coding sequence-embedded principle governs translational reading frame fidelity

Project description:Upon initiation at an AUG start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. Although some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known how the ribosome normally prevents spontaneous frameshift errors. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3’ end of 18S rRNA to scan the AUG-like codons after the decoding process. The internal mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a post-decoding mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes by minimizing the appearance of AUG-like codons in the frame 2. These results suggest an important layer of information embedded within the protein coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.

2016-04-12 | GSE80156 | GEO

Open reading frame phylogenetic analysis on the cloud.

Project description: Not available

| S-EPMC3647537 | biostudies-literature

Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome.

Project description: Not available

| S-EPMC10269785 | biostudies-literature

Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

Project description:The eIF2 initiation complex is central to maintaining a functional translation machinery. Extreme stress such as life-threatening sepsis exposes vulnerabilities in this tightly regulated system, resulting in an imbalance between the opposing actions of kinases and phosphatases on the main regulatory subunit eIF2α. Here, we report that translation shutdown is a hallmark of established sepsis-induced kidney injury brought about by excessive eIF2α phosphorylation and sustained by blunted expression of the counterregulatory phosphatase subunit Ppp1r15a. We determined that the blunted Ppp1r15a expression persists because of the presence of an upstream open reading frame (uORF). Overcoming this barrier with genetic approaches enabled the derepression of Ppp1r15a, salvaged translation and improved kidney function in an endotoxemia model. We also found that the loss of this uORF has broad effects on the composition and phosphorylation status of the immunopeptidome that extended beyond the eIF2α axis. Collectively, our findings define the breath and potency of the highly conserved Ppp1r15a uORF and provide a paradigm for the design of uORF-based translation rheostat strategies. The ability to accurately control the dynamics of translation during sepsis will open new paths for the development of therapies at codon level precision.

2021-12-22 | GSE191262 | 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