Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

C. elegans LC-MS/MS analysis with TMT labeling

ABSTRACT: Quantitative spatiotemporal proteomics mapping by Tandem Mass Tag labeling in live C. elegans

INSTRUMENT(S): Q Exactive

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Jinmin Liu

LAB HEAD: Yimon Aye

PROVIDER: PXD027730 | Pride | 2024-11-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DU_191126_HF_ges1_Hph10_Fr01.raw	Raw
	DU_191126_HF_ges1_Hph10_Fr02.raw	Raw
	DU_191126_HF_ges1_Hph10_Fr03.raw	Raw
	DU_191126_HF_ges1_Hph10_Fr04.raw	Raw
	DU_191126_HF_ges1_Hph10_Fr05.raw	Raw

Items per page:

1 - 5 of 39

Similar Datasets

C. elegans LC-MS/MS analysis with TMT labeling

Project description:Quantitative spatial proteomics mapping by Tandem Mass Tag labeling in live C. elegans

2024-11-05 | PXD052114 | Pride

Characterisation of a cell-free myxoid liposarcoma patient-derived xenograft scaffold model

Project description:Myxoid liposarcoma (MLS) is the second most common type of liposarcoma, and today few model systems to study the disease exists. To be able to model the disease in vitro, cell-free scaffolds from MLS patient-derived xenograft (PDX) models were generated. The MLS scaffolds were then used as a 3D growth platform for MLS cell lines to study the cancer microenvironments impact on cellular heterogeneity using RNA sequencing. Key components in the microenvironment have also been shown to influence the fraction of cellular subpopulations, such as cancer stem cells and migratory cells but also to promote aggressive features of cancers. Therefore, to better understand and characterize these scaffolds, protein analyses were performed and links between scaffold compositions and the induced gene expression profiles of the cells grown therein could be made. This model system provides a better insight to the composition of the cell-free cancer microenvironment in a rare disease, which can lead to identification of novel malignancy inducing properties in MLS.

2024-05-08 | PXD023792 | Pride

The Human Telomeric Proteome During Telomere Replication

Project description:Telomere shortening can cause detrimental diseases and contribute to aging. It occurs due to the end replication problem in cells lacking telomerase. In addition, recent evidence revealed that telomere shortening can be attributed to difficulties of the semi-conservative DNA replication machinery to replicate through the bulk of telomeric DNA repeats. To investigate telomere replication in a comprehensive manner, we developed QTIP-iPOND, which enables purification of the proteins that associate with telomeres during their replication. We identify in addition to the core replisome a large number of proteins that specifically associate with telomere replication forks and validate their importance.

2021-11-03 | PXD018712 | Pride

rs143348853 in vitro DNA pulldown

Project description:Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. We named these molecularly coordinated regions “variable chromatin modules” (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect an uncharacterized VCM-modulating non-coding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a big change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with long-range chromatin compaction and AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.

2022-04-21 | PXD029313 | Pride

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress

Transcription profiling of rat at pheochromocytoma cell line PC12 treated with trimethyltin at low and high doses

Project description:The rat pheochromocytoma cell line PC12 cells were cultured in complete DMEM till 80% confluence, then placed at 5000 cells per squared cm. Cells were then plated in 24-well plates for cell viability assay and in T75 flasks for RNA isolation. Medium was replaced with serum-free fresh medium for 12 hours prior to TMT treatment. Gene expression patterns were then analysed using Rat Expression Array 230A Experiment Overall Design: In this study we analize gene expression patterns in PC12 cells treated with Trimethyltin (TMT). We utilized control cells (untreated) and two different concentration (1 and 5) Experiment Overall Design: We used three biological replicates, for the three concentration tested, according to MIAME guidelines Experiment Overall Design: (total 9 chips were used in this study).

2009-04-29 | E-GEOD-5073 | biostudies-arrayexpress

C. elegans LC-MS/MS analysis by label-free quantification

Project description:Quantitative proteomics mapping by label-free quantification in live C. elegans

2024-11-05 | PXD052493 | Pride

Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles

Project description:Neisseria gonorrhoeae (GC) is a human-specific pathogen, and the agent of a sexually transmitted disease, gonorrhea. There is a critical need for new approaches to study and treat GC infections because of the growing threat of multidrug-resistant isolates and the lack of a vaccine. Despite the implied role of the GC cell envelope and membrane vesicles in colonization and infection of human tissues and cell lines, comprehensive studies have not been undertaken to elucidate their constituents. Accordingly, in pursuit of novel molecular therapeutic targets, we have applied isobaric tagging for absolute quantification coupled with liquid chromatography and mass spectrometry for proteome quantitative analyses. Mining the proteome of cell envelopes and native membrane vesicles revealed 533 and 168 common proteins, respectively, in analyzed GC strains FA1090, F62, MS11, and 1291.

2014-12-19 | PXD000549 | Pride

ER-Golgi membrane contact sites control the formation of plasma membrane lipid nanodomains required for anthrax intoxication

Project description:To promote infections, pathogens exploit host cell machineries including structural elements of the plasma membrane. Studying these interactions and identifying molecular players is an ideal way to gain insights into the fundamental biology of the host cell. Here, we used the anthrax toxin to screen a library of 1500 regulatory, cell surface, and membrane trafficking genes for their involvement in the intoxication process. We found that ER-Golgi localized proteins TMED2 and TMED10 are required for toxin oligomerization at the plasma-membrane of human cells, an essential step dependant on localization to cholesterol-rich lipid nanodomains. Biochemical, morphological and mechanistic analyses showed that TMED2 and TMED10 are essential components of a complex that operates the exchange of both cholesterol and ceramides at ER-Golgi membrane contact sites. Overall, this study of anthrax intoxication led to the discovery that lipid compositional remodelling at ER-Golgi interfaces fully controls the formation of functional membrane nanodomains at the cell surface.

2022-09-07 | PXD036511 | Pride

Proteomics of cell-free patient-derived scaffolds from breast cancer identify clinically relevant imprinted proteins and cancer-progressing properties

Project description:Breast cancer is a heterogenous disease that is difficult to model in vitro. Frozen primary breast cancers were decellularised to generate patient-derived scaffolds which are used to model 3D growth for cancer cell lines. The cell-free cancer microenvironments in the patient-derived scaffolds influence breast cancer cell line phenotypes and enrich for cells with cancer stem cell characteristics. Growth in patient-derived scaffold cultures also influenced the expression of epithelial-to-mesenchymal transition-related genes, and several gene expression changes in the model could be associated to clinical parameters of the original tumors and corresponding patients. Previous studies also demonstrated that the relative protein composition in the cell-free cancers were related to tumor grade and proliferation in cancer cells, suggesting that the relative proteomic composition varies between individual microenvironments. Therefore, we decellularised a larger breast cancer cohort to better characterize the cell-free microenvironments and potentially link to clinical features of the tumors and patients, which could be used to identify novel processes and targets that could be used to better model the disease or targeted in drug discovery.

2024-04-18 | PXD042671 | 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