Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Total RNA sequencing of AKAP12 knockdown cells

ABSTRACT: We compared gene expression in AKAP12 knockdown and control cells in the SW480 background.

ORGANISM(S): Homo sapiens

PROVIDER: GSE147739 | GEO | 2020/09/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Total RNA sequencing of AKAP12 knockdown cells

Project description:Total RNA sequencing of AKAP12 knockdown cells

| PRJNA616288 | ENA

Total RNA sequencing of RBMS1 knockdown cells

Project description:We compared gene expression in RBMS1 knockdown and control cells in the SW480 background.

2020-09-16 | GSE147741 | GEO

AKAP12 UV RNA immunoprecipitation followed by high throughput sequencing

Project description:Regulation of subcellular mRNA localisation is a fundamental biological mechanism, which adds a spatial dimension to the diverse layers of post-transcriptional control of gene expression. Insights into this phenomenon have been described in a multitude of cell types and across taxonomic kingdoms, highlighting its biological significance. The cellular compartment in which mRNAs are located may define distinct aspects of the encoded proteins, ranging from production rate and complex formation to localised activity. Ultimately, mRNA localisation supports compartmentalised mechanistic outputs that can respond to local stimuli, orient migration, or even shape cells. We used an unbiased method to profile the RNA-bound proteome in migrating endothelial cells and found that the plasma membrane (PM)-associated A-kinase anchor protein 12 (AKAP12) interacts with various mRNAs, including mRNAs encoding kinases with Actin remodelling activity. To identify transcripts bound by AKAP12, we carried out UV crosslinking experiments followed by RNA immunoprecipitation and high throughput sequencing. Our data offer novel insights in complex mechanisms of spatial control of gene expression.

2024-03-28 | GSE247682 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

Project description:Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage, is a multi-faceted protein affecting multiple malignant behaviors in cancer cells. The goals of this study are to compare the mRNA transcriptome differences between SW480 cells and HPSE-knockdown SW480 cells. Methods: mRNA profiles of SW480 cells and HPSE-knockdown SW480 cells were generated by deep sequencing, in triplicate, using Illumina.

2019-02-14 | GSE126504 | GEO

Expression data from SW480 cells with Gankyrin knockdown

Project description:We performed genome-wide screening using SW480 cells with Gankyrin knockdown on an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin. Transcriptional profiling with samples from SW480 cells that were infected with control or gankyrin shRNA. Two condition experiment: control shRNA (three replicates) and NFIL3 shRNA (three replicates)

2013-02-04 | E-GEOD-44029 | biostudies-arrayexpress

Transcriptome profiling of liver samples from WT and AKAP12 KO mice after inducing fibrosis resolution

Project description:AKAP12 KO mice showed reduced fibrosis resolution in DDC-induced hepatic fibrosis and resolution model. To compare gene expression profile between genotypes, transcriptome was analyzed by RNA sequencing.

2018-09-01 | GSE104030 | GEO

RNAi profiling by array of SW840 cells after Ezrin knockdown

Project description:Analysis of SW480 cells following knockdown of Ezrin using RNAi. Ezrin is a protein that regulate the organization of cytoskeleton. Ezrin KD SW480 was used to study the role of ezrin in colon cancer. Experiment Overall Design: Knockdown ezrin in SW480 cells and investigate the affection on cell migration and the downstream genes.

2008-06-11 | E-GEOD-11279 | biostudies-arrayexpress

Ezrin knockdown in SW480

2008-04-29 | GSE11279 | GEO

Endothelial deletion of EPH receptor A4 alters single-cell profile and Tie2/Akap12 signaling to preserve blood-brain barrier integrity

Project description:Neurobiological consequences of traumatic brain injury (TBI) result from a complex interplay of secondary injury responses and sequela that mediates chronic disability. Endothelial cells are important regulators of the cerebrovascular response to TBI. Our work demonstrates that genetic deletion of endothelial cell (EC)-specific EPH receptor A4 (EphA4) using conditional EphA4f/f/Tie2-Cre and EphA4f/f/VE-Cadherin-CreERT2 knockout (KO) mice, promotes blood-brain barrier (BBB) integrity and tissue protection, which correlates with improved motor function and cerebral blood flow recovery following controlled cortical impact (CCI) injury. scRNAseq of capillary-derived KO ECs showed increased differential gene expression of BBB-related junctional and actin cytoskeletal regulators, namely, A-kinase anchor protein 12, Akap12, whose presence at Tie2 clustering domains is enhanced in KO microvessels. Transcript and protein analysis of CCI-injured whole cortical tissue or cortical-derived ECs suggests EphA4 limits the expression of Cldn5, Akt, and Akap12 and promotes Ang2. Blocking the Tie2 receptor using sTie2-Fc, attenuated BBB and tissue protection and reversed Akap12 mRNA and protein levels in KO compared to WT cortical-derived ECs. Conversely, direct stimulation of Tie2 using Vasculotide, an angiopoietin-1 memetic peptide, phenocopied the neuroprotection. Finally, we report a noteworthy rise in soluble Ang2 in the sera of individuals with acute TBI, highlighting its promising role as a vascular biomarker for early detection of BBB disruption. Overall, we describe a novel contribution of the axon guidance molecule, EphA4, in mediating TBI microvascular dysfunction through negative regulation of Tie2/Akap12 signaling.

2023-09-24 | GSE240430 | GEO

Analysis of protein expression change upon RBMS1 knockdown

Project description:To assess how dpeletion of RBMS1 affects the proteome, SW480 colon adenocarcinoma cells expressing control or RBMS1 shRNAs were compared by Tandem Mass Tagging (TMT) protoemics.

2020-06-10 | PXD019478 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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