Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA219183 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Reverse phase protein array based protein profiling of breast cancer specimens
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Project description:The C10orf10 protein profiling of breast cancer specimens based on a tissue array
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Project description:From ~1,700 non-small cell lung cancer specimens collected at the MD Anderson Cancer Center over the years 1997 to 2005, we selected 914 tumors with detailed clinical and pathological information. We extracted RNA and DNA from frozen tissues using histology quality control from 700 cases. RNA was examined for quality using Agilent Bioanalyzer and RNA integrity number (RIN) was obtained for all specimens. A final selection of 275 tumor specimens was based on the following criteria: 1) Select mainly adenocarcinomas (n = 183) and squamous carcinomas (n = 80); 2) Tissue material contains at least 70% tumor by section examination; 3) within the tumor section, there should be at least 30% tumor cells (as opposed to stromal cells); 4) RIN should be at least 4.0 (range 0 - 10). Various profiling experiments were then performed including mRNA expression (this study), miRNA profiling, aCGH (Agilent), Reverse-phase protein array (RPPA), mutation analysis of 20 genes (Sequenom) and MS-MALDI-TOFF analysis.
2013-07-01 | GSE41271 | GEO
Project description:Glycoproteins comprise more than half of current FDA-approved protein cancer markers but the development of new glycoproteins as disease biomarkers has been stagnant. Here we present a pipeline to develop glycoproteins from extracellular vesicles (EVs) through integrating quantitative glycoproteomics with a novel reverse phase glycoprotein array, and then apply it to identify novel biomarkers of breast cancer. EV glycoproteomics show promise in circumventing the problems plaguing current serum glycoproteomics and allowed us to identify hundreds of glycoproteins that have not been identified in serum. We identified 1,453 unique glycopeptides representing 556 glycoproteins in EVs, among which 20 are significantly higher in breast cancer patients. We further applied a novel glyco-specific reverse phase protein array to quantify a subset of the candidates. Together, this study demonstrates the great potential of this integrated pipeline for biomarker discovery.
2018-04-26 | PXD007572 | Pride
Project description:From ~1,700 non-small cell lung cancer specimens collected at the MD Anderson Cancer Center over the years 1997 to 2005, we selected 914 tumors with detailed clinical and pathological information. We extracted RNA and DNA from frozen tissues using histology quality control from 700 cases. RNA was examined for quality using Agilent Bioanalyzer and RNA integrity number (RIN) was obtained for all specimens. A final selection of 275 tumor specimens was based on the following criteria: 1) Select mainly adenocarcinomas (n = 183) and squamous carcinomas (n = 80); 2) Tissue material contains at least 70% tumor by section examination; 3) within the tumor section, there should be at least 30% tumor cells (as opposed to stromal cells); 4) RIN should be at least 4.0 (range 0 - 10). Various profiling experiments were then performed including mRNA expression (this study), miRNA profiling, aCGH (Agilent), Reverse-phase protein array (RPPA), mutation analysis of 20 genes (Sequenom) and MS-MALDI-TOFF analysis. 275 lung cancer specimens collected at the MD Anderson Cancer Center were profiled on Illumina WG6-V3 expression arrays. Detailed clinico-pathological information were also collected.
2013-07-01 | E-GEOD-41271 | biostudies-arrayexpress
Project description:To investigate the novel functions of PTEN-L, we performed a Reverse Phase of Protein Array (RPPA) profiling on 468.Ctrl, 468.PTEN, and 468.PTEN-L sublines to compare cell signaling events between PTEN expression
2019-05-25 | GSE131746 | GEO
Project description:We report the development of a second-generation AKT degrader INY-05-040, which outperformed catalytic AKT inhibition both with respect to biochemical and cellular suppression of AKT/mTORC1-driven phenotypes in diverse breast cancer cell lines. Using multi-omic profiling and causal network integration, we demonstrate that the enhanced efficacy of INY-05-040 relies in part on potent downstream activation of stress mitogen activated protein kinase (MAPK) signaling. Systematic measurements of growth inhibition across 288 cancer cell lines confirmed the substantial improvement in potency for INY-05-040 compared to the first-generation AKT degrader (INY-03-041) and catalytic AKT inhibition with GDC-0068. Subsequent integration of breast cancer cell line-specific data with publicly available transcriptomic, proteomic and reverse phase protein array (RPPA) measurements revealed that decreased sensitivity to INY-05-040 correlates with a high baseline activation of inflammatory/stress signaling pathways. Collectively, our data uncover a unique mechanism of breast cancer cell line sensitivity to AKT degradation, further suggesting that the efficacy of catalytic AKT inhibition may be enhanced by activation of stress MAPKs in breast cancer cells with low baseline activity of these components.
2022-10-15 | GSE206388 | GEO