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

YBX1-dependent LNA-tRF-mediated modulation of gene expression under hypoxia

ABSTRACT: In order to test whether inhibition of tRFs induced under hypoxia would counteract the YBX1-dependent reduction of target transcripts, we used transient transfection of antisense locked-nucleic acids (pooled LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr under hypoxia followed by microarray profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected (as a pool) in control and YBX1-knockdown cells under hypoxia to assess the consequences of inhibiting tRFs induced in hypoxic MDA-parental cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Hani Goodarzi

PROVIDER: E-GEOD-63563 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

YBX1-dependent LNA-tRF-mediated modulation of gene expression

2015-05-08 | E-GEOD-63564 | biostudies-arrayexpress

YBX1-dependent LNA-tRF-mediated modulation of transcript stability

Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by alpha-amanitine treatment, RNA extraction at time points 0 and 8hr post-treatment, and transcriptomic profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets whose stabilities are modulated due to tRF loss-of-function. We used alpha-amanitine mediated inhibition of RNA-polymerase to measure transcript stability across the entire transcriptome.

2015-05-08 | E-GEOD-63565 | biostudies-arrayexpress

YBX1-dependent LNA-tRF-mediated modulation of gene expression under hypoxia

Project description:In order to test whether inhibition of tRFs induced under hypoxia would counteract the YBX1-dependent reduction of target transcripts, we used transient transfection of antisense locked-nucleic acids (pooled LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr under hypoxia followed by microarray profiling.

2015-05-08 | GSE63563 | GEO

YBX1-dependent LNA-tRF-mediated modulation of gene expression

2015-05-08 | GSE63564 | GEO

YBX1-dependent LNA-tRF-mediated modulation of transcript stability

2015-05-08 | GSE63565 | GEO

Inter-organellar communication by a mitochondrial tRNA regulates nuclear metabolic transcription (RNA-Seq)

Project description:To assess transcriptomic changes that occur upon mito-tRNA Asparagine inhibition, MDA-MB-231 cells were transfected with either a non-targeting control locked nucleic acid (LNA), two independent LNAs targeting mito-tRNA Asparagine, or an LNA against mito-tRNA Lysine.

2023-07-01 | GSE213171 | GEO

The ULK3 kinase is a key determinant of keratinocyte self-renewal and tumorigenesis targeting the arginine methylome

Project description:Epigenetic mechanisms oversee epidermal homeostasis and oncogenesis. The identification of kinases controlling these processes has direct therapeutic implications. We show that ULK3 is a nuclear kinase with elevated expression levels in squamous cell carcinomas (SCCs) arising in multiple body sites, including skin and Head/Neck. ULK3 loss by gene silencing or deletion reduces proliferation and clonogenicity of human keratinocytes and SCC-derived cells and affects transcription impinging on stem cell-related and metabolism programs. Mechanistically, ULK3 directly binds and regulates the activity of two histone arginine methyltransferases, PRMT1 and PRMT5 (PRMT1/5), with ULK3 loss compromising PRMT1/5 chromatin association to specific genes and overall methylation of histone H4, a shared target of these enzymes. These findings are of translational significance, as downmodulating ULK3 by RNA interference or locked antisense nucleic acids (LNAs) blunts the proliferation and tumorigenic potential of SCC cells and promotes differentiation in two orthotopic models of skin cancer.

2022-11-14 | MTBLS5155 | MetaboLights

Quantifying the transcriptional effects of lncRNA depletion in HeLa cells with RNA-seq

Project description:Long noncoding RNAs (lncRNAs) are a major transcriptional output of the mammalian genome, yet their functions are poorly characterized. In this experiment, we used RNA interference (RNAi) and locked nucleic acid antisense oligonucleotides (LNAs) to deplete the lncRNAs LINC00899 and C1QTNF1-AS1 (C1) in HeLa cells. Both of these lncRNAs are of interest as their depletion results in mitotic delay, suggesting a role in mitotic progression. After depletion of each lncRNA with RNAi or LNAs, we performed high-throughput RNA sequencing and tested for differential expression compared to negative control samples (using control siRNAs or negative control LNAs) to identify downstream regulatory targets of each lncRNA. We generated 3-4 replicates for each condition, spread across multiple batches and experiments. Samples with the same batch number were treated at roughly the same time (within the same month), while the experiment number is nested within batch and refers to cells treated on the same day. Samples were pooled and sequenced across multiple lanes, yielding 8-9 technical replicates per sample.

2019-03-01 | E-MTAB-7432 | biostudies-arrayexpress

Study of the role of miR-205 in prostate epithelial cells

Project description:Gene expression has been assessed on RWPE-1 cells, derived from normal prostate, upon silencing of miR-205 by an antisense locked nucleic acid. RWPE-1 cells were transfected in triplicate either with 100nM of an antisense locked nucleic acid targeting miR-205 (LNA-205) or a scrambled oligomer (LNA-Scr). Gene expression was assessed 72h after transfection.

2012-06-11 | E-GEOD-29782 | biostudies-arrayexpress

YBX1-dependent hypoxia-induced modulation of gene expression

Project description:In order to identify YBX1-dependent targets that are modulated under hypoxic conditions, we used control and YBX1 knockdown cells grown under normoxia and hypoxia to profile gene expression levels. Control and YBX1-knockdown cells were grown and profiled under hypoxia and normoxia to identify YBX1-dependent hypoxia-induced target transcripts.

2015-05-08 | E-GEOD-63562 | 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