Browse
Submit Data
Databases
API
Help

Dataset Information

306 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of TPA on focal adhesion composition

ABSTRACT: Effect of a tumor promoter TPA on collagen IV based focal adhesions from CHO cells expressing human integrin alpha1 with activating mutation E317A

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Cricetulus Griseus (chinese Hamster) (cricetulus Barabensis Griseus)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Pekka Rappu

LAB HEAD: Jyrki Heino

PROVIDER: PXD003153 | Pride | 2016-07-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Tumor promoter PMA enhances kindlin-2 and decreases vimentin recruitment into cell adhesion sites.

Salmela Maria M Rappu Pekka P Lilja Johanna J Niskanen Henri H Taipalus Elina E Jokinen Johanna J Heino Jyrki J

The international journal of biochemistry & cell biology 20160629

Phorbol diester PMA (phorbol 12-myristate 13-acetate) is a well-known promoter of tumor progression. PMA also regulates cell adhesion by several mechanisms including conformational activation of integrins and integrin clustering. Here, PMA was shown to induce lamellipodia formation and reorganization of the adhesion sites as well as actin and vimentin filaments independently of integrin preactivation. To further analyze the mechanism of PMA action, the protein composition in the α1β1 integrin/co ...[more]

PMID: 27373681

Similar Datasets

Podocyte Focal Adhesion Proteome

Project description:Expression proteomics analysis of focal adhesion complexes isolated from a human immortalized podocyte cell line.

2018-12-14 | PXD010626 | Pride

Transcription profiling of rats treated with transient focal ischemia

Project description:Large clinical studies have shown that AT1 receptor blockers (ARBs) reduce the incidence of stroke in patients at risk. However, there is controversy about the underlying pathomechanisms. To get a closer insight into the effects of ARBs in stroke on molecular level, gene expression pattern was compared in the ischemic brain areas of Candesartan pre-treated (0,2 mg/kg bwt., 5 days, s.c.) versus vehicle treated, normotensive, adult rats after middle carotid artery occlusion (MCAO). Candesartan significantly improved neurological outcome (as estimated by Garcia-scale) 24 h and 48 h after stroke and reduced infarct volume by about 40% compared to vehicle. Experiment Overall Design: For gene expression profiling, RNA of two animals per group was pooled and forwarded to preparation of the labeled targets for the micro array experiment. For each biological condition two independent pools were hybridised onto Affymetrix RAE 230A arrays.

2008-06-12 | E-GEOD-4206 | biostudies-arrayexpress

Expression of SUDHL-1 cell line treated by ALK inhibitors

Project description:In this study we compared the effects of ALK inhibitor on the gene expression, activation of cell signaling pathways, and functional properties of cells derived from a patient with Anaplastic Large Cell Lymphoma. we used microarrays to map the genome-wide gene expression patterns in ALK+TCL cells in response to ALK inhibition. The ALK+TCL Sudhl-1 cell line was treated in triplicates with the ALK inhibitor, CEP-14083, or the compound's solvent for 6 h. The isolated RNA was reverse-transcribed, biotin-labeled, and hybridized to the U133 Plus 2.0 array chips (Affymetrix). Microarray data were normalized using the MAS5 algorithm and analyzed using Partek GS (Partek).

2013-10-31 | E-GEOD-50803 | biostudies-arrayexpress

Proteome and phosphoproteome of hippocampus after focal cerebral ischemia 2 h in mice

Project description:We obtained the profiles of neuronal phosphoproteome after cerebral ischemia onset by isolating mice hippocampus. Hippocampus combined from either ten sham or ten focal cerebral ischemia 2 h mice were lysed, digested, labeled with different TMT tags, then pooled and analyzed by LC/LC-MS/MS. Five percent of the pool was used for whole proteome analysis, and the remaining 95% was subjected to phosphoproteome profiling. In total, we quantified 5,174 proteins and 9,062 phosphopeptides. Interesting, 21 proteins were upregulated and 7 proteins were downregulated in hippocampus lysates of cerebral ischemia 2 h relative to sham base on fold change. S100a9, Alpha-2-HS-glycoprotein (Ahsg), Fibrinogen beta chain (Fga) and Complement Component C3(c3) are the top significantly changed, which were highly consistent with previous reports in cerebral ischemia injury. Using wolfpsort software to analysis the Subcellular Location, 57% of detected proteins were location to extracellular, 15% were cytoplasmic protein, another 11% were transport to nucleus, and the others were location to plasma membranes (10%), mitochondria (4%) and endoplasmic reticulum (3%). Moreover,184 phosphorylation sites of 135 proteins were upregulated and 689 phosphorylation sites of 420 proteins were downregulated in hippocampus during cerebral ischemia 2 h compare with sham operation. Employing wolfpsort software analysis the subcellular location, 50% of phosphorylated proteins were location to nucleus, 26% were cytoplasmic protein, another 16% were transport to plasma membranes, and the others were location to mitochondria (4%), extracellular (3%) and cytoskeleton (1%). Motif analysis showed that 85% were belongs to serine-type phosphorylation, about 14 were threonine-type phosphorylation and 1% were tyrosine-type phosphorylation.

2022-03-14 | PXD027145 | Pride

Multi-omics characterization of MEK inhibitor resistant pancreatic cancer based on a genetically engineered mouse model-derived in vitro system

Project description:Tumor heterogeneity and therapy resistance are hallmarks of pancreatic ductal adenocarcinoma (PDAC). Emerging evidence supports treatment-induced resistance to be a multifactorial process mediated by cellular plasticity involving epigenetic regulation. Here, we used a multi-omics approach to analyze in detail molecular mechanisms underlying MEK inhibitor (MEKi) resistance. Therefore, we characterized different cell stages (parental, MEKi resistant, reverted after different passages of drug withdrawal) in primary cell lines derived from a genetic PDAC mouse model, thereby minimizing inter-individual heterogeneity that could distort genome-wide analyses.

2024-01-26 | PXD018093 | Pride

The effect of XUESAITONG on gene expression profile after focal cerebral ischemia in rats

Project description:Xuesaitong injection (XST), a standardized patent Chinese medicine of Panax notoginseng roots (Sanqi in Chinese), has long been used for effective prevention and treatment of stroke in China. However, the mechanisms underlying its effects against ischemic stroke are still poorly understood. In this study, we focused on the polypharmacology of XST against ischemic stroke with a XST-regulated stroke network analysis. Male Sprague Dawley rat model of MCAO and reperfusion were administered XST for 7 days while the control group was not treated. Three conditions were compared with three replicates each. These are: (1) sham; (2) model (3) XST treatment. Whole genome microarray analysis was performed using Affymetrix rat Genome 230 2.0 chips.

2014-09-23 | E-GEOD-61616 | biostudies-arrayexpress

Quantitative proteome profiling of Leishmania donovani after hypericin treatment

Project description:Hypericin, a novel inhibitor of spermidine synthase of Leishmania donovani, has been found to cause necrotic like death of the parasite. Hypericin treatment has indicated the importance of spermidine in pathways other than redox metabolism of Leishmania parasite. We have used label free quantitative proteomics approach to compare the alteration in expression of proteins in untreated and hypericin treated Leishmania promastigotes.

2016-04-21 | PXD003815 | Pride

ENCODE Transcript Mapping for Total RNA from Human NB4 Cells untreated, treated with RA, and treated with TPA

Project description:Transcript Mapping on Affymetrix ENCODE arrays for Total RNA from 4 different samples (2 or 3 technical replicates of each). All of the four same NB4 samples have also been treated with Retanoic Acid (RA) (2 or 3 technical replicates of each). Three of the four same NB4 samples have also been treated with TPA (2 or 3 technical replicates of each). RA treated NB4 cells can be partially differentiated to Neutrophils and TPA treated NB4 cells can be differentiated to Monocytes. Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays Keywords: parallel sample

2010-06-10 | E-GEOD-2679 | biostudies-arrayexpress

phosphoproteome of hippocampus after focal cerebral ischemia 1.5 h and reperfusion 24 h in mice

Project description:We obtained the profiles of neuronal phosphoproteome after cerebral ischemia and reperfusion by isolating mice hippocampus. Hippocampus combined from either nine sham or nine focal cerebral ischemia 1.5 h and reperfusion 24 h (IR) mice were lysed, digested, labeled with different TMT tags, then pooled and analyzed by LC/LC-MS/MS. In total, we quantified 7,865 phosphopeptides,179 phosphorylation sites of 129 proteins were upregulated and 843 phosphorylation sites of 494 proteins were downregulated in hippocampus during cerebral ischemia 2 h compare with sham operation.

2024-02-15 | PXD033851 | Pride

Proteome of hippocampus after focal cerebral ischemia 1.5 h and reperfusion 24 h in mice

Project description:We obtained the profiles of neuronal proteome after cerebral ischemia and reperfusion by isolating mice hippocampus. Hippocampus combined from either nine sham or nine focal cerebral ischemia 1.5 h and reperfusion 24 h (IR) mice were lysed, digested, labeled with different TMT tags, then pooled and analyzed by LC/LC-MS/MS. In total, we quantified 5,059 proteins. We identified 142 differentially expressed proteins (t-test, p-value<0.05) after IR compared to sham groups. The results showed that 92 proteins were upregulated, and 50 proteins were downregulated after IR compared to sham groups. Gene ontology (GO) enrichment analysis of differentially expressed proteins between sham and IR groups. The results showed that the biological process of most of upregulated genes linked with immune inflammatory related responses were increased. And KEGG pathway analysis for upregulated genes showed that multiple immune inflammatory response pathways also increased significantly, such as TNF-signaling, NF-κB signaling and cytokine-cytokine receptor interaction, as well as NOD-like receptor signaling, and toll-like receptor signaling.

2024-02-15 | PXD033938 | 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