Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The proteome of clear cell ovarian carcinoma

ABSTRACT: Clear cell ovarian carcinoma (CCOC) is the second most common subtype of epithelial ovarian carcinoma. Late stage CCOC is not responsive to gold-standard chemotherapy and result in suboptimal outcome for patients. In-depth molecular insight is urgently needed to stratify the disease and drive therapeutic development. We conducted global proteomics in 192 cases of CCOC comparing to other epithelial ovarian carcinoma subtypes.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Ovary

SUBMITTER: Gian Luca Negri

LAB HEAD: Gregg Morin

PROVIDER: PXD032355 | Pride | 2022-09-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Huntsman_BMBP_SS_CCOC_B10_F1.raw	Raw
	Huntsman_BMBP_SS_CCOC_B10_F10_20190822233007.raw	Raw
	Huntsman_BMBP_SS_CCOC_B10_F11.raw	Raw
	Huntsman_BMBP_SS_CCOC_B10_F12.raw	Raw
	Huntsman_BMBP_SS_CCOC_B10_F2.raw	Raw

Items per page:

1 - 5 of 464

Similar Datasets

Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes

Project description:Despite the advancement of genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information. Formalin-fixed paraffin-embedded (FFPE) tissue specimens are widely available and can be directly linked to extended clinical outcomes. We performed comprehensive proteomic profiling of 300 FFPE breast cancer surgical specimens, 75 of each PAM50 subtype, with linked clinical outcomes. Using our highly sensitive SP3-Clinical Tissue Proteomics platform, we quantified 4214 proteins across all 300 samples. The analysis identified a distinct proteomic group characterized by high expression of immune response proteins and favorable survival rates. Four clinically distinct proteomic clusters within samples classified as triple negative breast cancer by immunohistochemistry had features of “basal-immune hot”, “basal-immune cold”, “mesenchymal”, and “luminal androgen receptor”. Our proteomic analysis characterizes the heterogeneity of breast cancer in a clinically-applicable manner, identifies potential biomarkers and therapeutic targets, and provides a resource for clinical breast cancer classification.

2022-02-22 | PXD024322 | 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

miRNA profiling of LNCaP cells treated with bortezomib or celastrol against untreated control group

Project description:This study is designed for exploring miRNAs affected by proteasome inhibitor treatment. LNCaP cells were treated with 100nM bortezomib or 2.5 uM celastrol for 12 hrs, and was subjected to miRNA profiling assay.

2020-12-30 | E-MTAB-6215 | biostudies-arrayexpress

Proteome analyses of two ovarian clear cell carcinoma cell lines with or without ARID1A manipulation

Project description:ARID1A, which encodes a component of the SWI/SNF chromatin-remodeling complex, is commonly mutated in ovarian clear cell carcinoma and many other cancer types. We used label-free LC-MS/MS to identify ARID1A-dependent proteome changes in ovarian clear cell carcinoma cell lines. In our first analysis, we compared ARID1A-wildtype ovarian clear cell carcinoma cell line OVCA429 with or without ARID1A CRISPR knockout. In a complementary analysis, we compared ARID1A-mutated ovarian clear cell carcinoma cell line OVISE with or without ARID1A overexpression using a tet-inducible promoter.

2016-07-13 | MSV000079904 | MassIVE

SP3 protocol for proteomic plant sample preparation prior LC-MS/MS

Project description:Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the ﬁlter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient two-hour SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust amount of beads, binding and rinsing conditions, or digestion parameters.

2021-02-26 | PXD022688 | Pride

Changes in the tumor microenvironment mark transition from serous borderline tumor to low grade serous carcinoma

Project description:Low grade serous ovarian cancer (LGSC) is a rare subtype of ovarian cancer, characterized by a slow growth rate, resistance to current treatment regimens, multiple recurrences and poor survival. LGSC arise from serous borderline tumor (SBT), however the mechanism of transformation is poorly understood. To better understand the biology of serous ovarian tumors, we performed whole proteome profiling of LGSC, SBT and the more common high grade serous (HGSC) ovarian tumors. Proteins associated with the tumor microenvironment were differentially expressed between LGSC and SBT or HGSC. In particular, fibroblast activation protein (FAP), a protein expressed in cancer associated fibroblasts, is abundantly expressed in LGSC. Furthermore, Tregs and M2 macrophages are more abundant in the stroma of LGSC compared to SBT. Together these data suggest that the tumor microenvironment provides a supportive environment for LGSC tumorigenesis and progression, and that targeting the tumor microenvironment of LGSC may be a viable therapeutic strategy.

2024-08-15 | PXD046360 | Pride

Cell-type specific phenotypic characterization of Lyve1+ perivascular macrophages and Sall1+ microglia pooled from PBS and amyloid-β-injected mice

Project description:RiboTag-based translatome analysis of pooled oAβ and PBS-challenged brain homogenates of Cx3cr1ccre:Lyve1ncre (n=8 mice) and Cx3cr1ccreSall1ncre:RiboTag-mice (n=4 mice).

2023-01-10 | E-MTAB-12515 | biostudies-arrayexpress

Linking planar polarity signaling directly to actomyosin contractility during vertebrate neurulation

Project description:Actomyosin contractility represents an ancient feature of eukaryotic cells participating in many developmental and homeostasis events, including tissue morphogenesis, muscle contraction, and cell migration, with dysregulation implicated in various pathological conditions, such as cancer. At the molecular level, actomyosin comprises actin bundles and myosin motor proteins that are sensitive to posttranslational modifications like phosphorylation. While the molecular components of actomyosin and its regulation are well understood, the coordination of contractility by extracellular and intracellular signals, particularly from cellular signaling pathways, remains incompletely elucidated. This study focuses on planar cell polarity (PCP) signaling, previously associated with actomyosin contractility during vertebrate neurulation. Contrary to previous studies, our investigation reveals that main cytoplasmic PCP proteins, Prickle and Dishevelled, interact directly with key actomyosin components such as myosin light chain (MLC), leading to its phosphorylation and localized activation. Through relevant in vitro and in vivo models, we demonstrate that these PCP proteins function not merely passively and indirectly as previously reported, but that they actively control actomyosin contractility by acting as scaffold proteins, orchestrating the necessary machinery for contractility. These findings unveil a direct link of PCP signaling in crucial actomyosin contractility processes through MLC that are relevant to vertebrate neurulation and potentially beyond.

2024-09-19 | PXD052350 | Pride

Genetically modified ID8 cells to study the role of GBP1 in ovarian cancer

Project description:Genetically modified ovarian cancer cells were used to study the role of GBP1. Proteomics-based thermal stability assay (CETSA) was performed on GBP1 knockdown and overexpressing ID8 ovarian cancer cells. Shotgun proteomics was also performed on these cells.

2024-01-26 | PXD040444 | 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