Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of ARF regulatory molecules co-immunoprecipitating with human SDC4 (huSDC4)

ABSTRACT: Proteomic analysis of ARF regulatory molecules co-immunoprecipitating with human SDC4 (huSDC4) from Syn4WT, Syn4-/-, Syn4Y180E and Syn4Y180L MEFs. Peptide analysis by LC-MS/MS was performed using an UltiMate 3000 Rapid Separation LC (Dionex Corporation) coupled to an Orbitrap Elite mass spectrometer (Thermo Fisher).

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Fibroblast

DISEASE(S): Disease Free

SUBMITTER: Mark Morgan

LAB HEAD: Mark Morgan

PROVIDER: PXD046898 | Pride | 2023-11-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20120524_MM_E1.raw	Raw
	20120524_MM_E10.raw	Raw
	20120524_MM_E11.raw	Raw
	20120524_MM_E12.raw	Raw
	20120524_MM_E13.raw	Raw

Items per page:

1 - 5 of 89

Publications

Systemically administered wound-homing peptide accelerates wound healing by modulating syndecan-4 function.

Maldonado Horacio H Savage Bryan D BD Barker Harlan R HR May Ulrike U Vähätupa Maria M Badiani Rahul K RK Wolanska Katarzyna I KI Turner Craig M J CMJ Pemmari Toini T Ketomäki Tuomo T Prince Stuart S Humphries Martin J MJ Ruoslahti Erkki E Morgan Mark R MR Järvinen Tero A H TAH

Nature communications 20231206 1

CAR (CARSKNKDC) is a wound-homing peptide that recognises angiogenic neovessels. Here we discover that systemically administered CAR peptide has inherent ability to promote wound healing: wounds close and re-epithelialise faster in CAR-treated male mice. CAR promotes keratinocyte migration in vitro. The heparan sulfate proteoglycan syndecan-4 regulates cell migration and is crucial for wound healing. We report that syndecan-4 expression is restricted to epidermis and blood vessels in mice skin w ...[more]

PMID: 38057316

Similar Datasets

Comparison of adhesion complex-associated proteins in MDA-MB-231 cells in a 2D vs 3D microenvironment

Project description:Cell invasion and metastasis is a multi-step process, initiated by the acquisition of a migratory phenotype and the ability to move through differing and complex 3D extracellular environments. In this study we set out to identify the parameters required for invasive cell migration in 3D environments. Cells interact with the extracellular matrix via transmembrane-spanning integrin adhesion complexes. We establish a technique to determine the composition of cell-matrix adhesion complexes in invasive breast cancer cells in 3D matrices and on 2D surfaces and identify an interaction complex that is enriched in 3D adhesion sites and required for invasive migration.

2024-02-07 | PXD043063 | Pride

Nuclear nucleolin interactome analysis

Project description:Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cell’s compartments. NCL has been shown to play important roles in a variety of essential functions among which ribosome biogenesis, gene expression and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 binding partners of NCL, among which, a 100 of them, were specifically found associated to NCL independently of the presence of RNA.

2016-04-11 | PXD003554 | Pride

Combining laser capture micro-dissection and proteomics reveals an active translation machinery controlling invadosome formation

Project description:We developed a method that combines laser micro-dissection and mass spectrometry, enabling the analysis of subcellular structures in their native state based on low amounts of input material. Using this combinatorial method, we showed that invadosomes contain specific components of the translational machinery, in addition to known marker proteins.

2018-10-19 | PXD009390 | Pride

ChIP-seq. analysis of pan-histone 3 acetylation in Romidepsin treated TCam-2

Project description:ChIP-seq. analysis of TCam-2 16 h after 10 nanomolar Romidepsin application. DMSO treated cells were used as controls. For ChIP, an antibody against histone H3 pan-acetylation was used. These data are part of the article 'The Histone Deacetylase Inhibitor Romidepsin Efficiently Targets Cisplatin-resistant Germ Cell Cancer Cells via Downregulation of the SWI/SNF-Complex Member ARID1A' (Nettersheim et al., 2016). TCam-2 cells treated for 16h with romidepsin or the solvent were fixed by formaldehyde solution and further processed by Active Motif, including DNA shearing by sonication, chromatin-immunoprecipitaion, library generation and sequencing (NextSeq 500, Illumina). Pooled input DNA of each sample including spike-in Drosophila DNA was used as controls and for normalization. The 75-nt sequence reads were mapped against the genome using BWA algorithm. Duplicate reads were removed. Only peaks that align with no more than 2 mismatches and map uniquely to the genome were used for further analysis. Intervals / peaks were identified by the MACS peak finding algorithm (cutoff p-value 1x10-7) including ENCODE blacklist filtering

2016-09-01 | E-GEOD-78262 | biostudies-arrayexpress

Arabidopsis FTSH11 mutant

Project description:The membrane-integrated metallo-protease FtsH11 of Arabidopsis thaliana is proposed to be dual targeted to mitochondria and chloroplasts. A bleached phenotype was observed in ftsh11 grown at long days or continuous light, pointing to disturbances in the chloroplast. Under these growth conditions the morphology of the chloroplast became drastically altered, accompanied by a drop of NPQ, and the amount of PSI decreased relative to PSII. The abundance of plastidic proteins, especially of photosynthetic proteins, was altered in ftsh11 even during growth in normal conditions and short days. FtsH11 is crucial for chloroplast structure and function during growth in prolonged photoperiod . In chloroplasts FtsH11 was found to be located exclusively in the chloroplast envelope. Thanks to proteomic analyses, the Tic22-like protein and YGGT, both chloroplast proteins of unknown function, are proposed to be the substrates of FtsH11 .

2022-03-03 | PXD002969 | Pride

Proteomic analysis of FBXL6 interacting proteome

Project description:FBXL6 is a E3 ubiquitin ligase that we suspected to be involved in mitochondrial functions. We have investigated the specific interactome of this E3 by transfecting HEK cells with Flagged-FBXL6, or with b-gal (control). After flag immunoprecipiation, specific interacting proteome was identified by mass spectrometry and discriminate from control IP.

2023-09-25 | PXD037248 | Pride

Proteomic analysis of BioID experiments performed with Toxoplasma gondii MyoJ protein tagged with TurboID in tachyzoites

Project description:The aim of the project was to identify proteins of the basal complex of Toxoplasma gondii using MyoJ as bait

2022-11-01 | PXD035106 | Pride

Enrichment and mass spectrometry analysis of TbTAX-1-interacting or TbTTC29-interacting proteins by co-immunoprecipitation

Project description:Study of Trypanosoma ZMYND12’s ortholog (TbTAX-1) confirmed an axonemal localization of the protein and knockdown of TbTAX-1 using RNAi induced dramatic flagellar motility defects as observed in human. Co-immunoprecipitation assays and ultra-structure expansion microscopy in Trypanosoma brucei then formally demonstrated that ZMYND12 and TTC29 directly interact and belong to the same axonemal complex. Subsequent comparative proteomics analysis in Trypanosoma and Ttc29 KO mice models also identified DNAH1 as a new interacting protein of both ZMYND12 and TTC29 proteins. These data evidenced the critical role of ZMYND12 for flagellum function and assembly in humans and Trypanosoma through its interaction with other axonemal partners such as TTC29 and DNAH1 in the same complex.

2023-11-01 | PXD039470 | Pride

Analyses of FBXL6 interaction with newly synthesized proteins.

Project description:HEK cells were grown in light media for two weeks. One day before experiments, cells were transfected with FBXL6-flag or B-gal (control). At t=0, cells were switched to heavy media for 3h and then Flag immunoprecipitation were performed. Pulled down protein were analyzed by mass spectrometry.

2023-09-25 | PXD037602 | Pride

Proteomic analysis of melanoma resistant cells transfected with siRNA targeting DDR2 or treated with DDR2 inhibitor or Dasatinib

Project description:Combined therapy with anti-BRAF plus anti-MEK is currently used as first-line treatment of patients with metastatic melanomas harboring the somatic BRAF V600E mutation. However, the main issue with targeted therapy is the acquisition of tumor cell resistance. In 70% of resistant melanoma cells, the resistant process consists in epithelial-to-mesenchymal transition (EMT). This process called phenotype switching makes melanoma cells more invasive. Its signature is characterized by MITF low, AXL high, and actin cytoskeleton reorganization through RhoA activation. In parallel of this phenotype switching phase, the resistant cells exhibit an anarchic cell proliferation due to hyper-activation of the MAP kinase pathway. We show that a majority of human melanoma overexpress discoidin domain receptor 2 (DDR2) after treatment. The same result was found in resistant cell lines presenting phenotype switching compared to the corresponding sensitive cell lines. We demonstrate that DDR2 inhibition induces a decrease in AXL expression and reduces stress fiber formation in resistant melanoma cell lines. In this phenotype switching context, we report that DDR2 control cell and tumor proliferation through the MAP kinase pathway in resistant cells in vitro and in vivo. Therefore, inhibition of DDR2 could be a new and promising strategy for countering this resistance mechanism.

2023-05-02 | PXD028292 | Pride

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