Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-Wide Characterization of Pancreatic Adenocarcinoma Patients Using Next Generation Sequencing

ABSTRACT:

In this study, we whole genome sequenced tumor/normal pairs from three pancreatic adenocarcinoma patients to separately characterize each patient with respect to somatic alterations. For 2 patients for whom tumor RNA was available, we also performed RNA sequencing to evaluate gene expression changes. While additional sequencing is needed to improve our understanding of the disease, the information acquired from this study contributes to our knowledge base on pancreatic cancer and helps to establish a foundation for identifying and developing more efficacious treatments for patients.

PROVIDER: phs000550.v1.p1 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing.

Liang Winnie S WS Craig David W DW Carpten John J Borad Mitesh J MJ Demeure Michael J MJ Weiss Glen J GJ Izatt Tyler T Sinari Shripad S Christoforides Alexis A Aldrich Jessica J Kurdoglu Ahmet A Barrett Michael M Phillips Lori L Benson Hollie H Tembe Waibhav W Braggio Esteban E Kiefer Jeffrey A JA Legendre Christophe C Posner Richard R Hostetter Galen H GH Baker Angela A Egan Jan B JB Han Haiyong H Lake Douglas D Stites Edward C EC Ramanathan Ramesh K RK Fonseca Rafael R Stewart A Keith AK Von Hoff Daniel D

PloS one 20121010 10

Pancreatic adenocarcinoma (PAC) is among the most lethal malignancies. While research has implicated multiple genes in disease pathogenesis, identification of therapeutic leads has been difficult and the majority of currently available therapies provide only marginal benefit. To address this issue, our goal was to genomically characterize individual PAC patients to understand the range of aberrations that are occurring in each tumor. Because our understanding of PAC tumorigenesis is limited, eva ...[more]

PMID: 23071490

Similar Datasets

Characterization of Pancreatic Adenocarcinoma Patients Using NGS

Project description:<p>In this study, we whole genome sequenced tumor/normal pairs from three pancreatic adenocarcinoma patients to separately characterize each patient with respect to somatic alterations. For 2 patients for whom tumor RNA was available, we also performed RNA sequencing to evaluate gene expression changes. While additional sequencing is needed to improve our understanding of the disease, the information acquired from this study contributes to our knowledge base on pancreatic cancer and helps to establish a foundation for identifying and developing more efficacious treatments for patients.</p>

| phs000550 | dbGaP

In-depth analysis of the pancreatic extracellular matrix during development for next generation tissue engineering

Project description:The pancreas is a complex organ consisting of differentiated cells and extracellular matrix (ECM), which together enable its functions, including exocrine secretion and hormone production. Alt-hough much is known about the intrinsic factors that control pancreas development, under-standing of the microenvironment surrounding pancreatic cells remains incomplete. This envi-ronment is composed of various cells and ECM components, which play a critical role in main-taining tissue organization and homeostasis. In this study, we applied mass spectrometry to identify and quantify the ECM composition of the developing pancreas at embryonic E14.5 and perinatal P1 stages. Our proteomic analysis identified 160 ECM proteins that displayed a dynamic expression profile with a shift in collagens and proteoglycans. Furthermore, we used atomic force microscopy to measure the biomechanical properties of the ECM and found that the whole pan-creas ECM is relatively soft with no significant change during pancreas maturation. Finally, we developed a decellularization protocol for P1 pancreatic tissues, which preserved the 3D organi-zation of the ECM and can be used for recellularization studies. Our findings provide insights into the composition and biomechanics of the pancreatic embryonic and perinatal ECM, offering a foundation for future studies investigating the dynamic interactions between the ECM and pan-creatic cells.

2023-06-19 | PXD042423 | Pride

Skeletal Muscle Fibrosis in Pancreatic Cancer Patients with Respect to Survival

Project description:Skeletal Muscle Fibrosis in Pancreatic Cancer Patients with Respect to Survival

| PRJNA540621 | ENA

Next generation sequencing (NGS) facilitates quantitative analysis of miRNA expression

Project description:Using NGS approach we performed the search of multiple sclerosis-related miRNAs. We used PBMC as an informative and easily accessible biological material. To exclude bias in miRNA expression levels caused by disease modifying therapies, miRNA profiling was performed in treatment-naïve RRMS patients. Taking into account hypothetic gender specificity in disease pathogenesis we compared miRNA expression in RRMS patients and HCs separately for men and women. MiRNA profiling in men identified 32 differentially expressed miRNAs, which passed threshold for multiple corrections and may be attributed to MS-related. At the same time we did not find well-defined MS-specific miRNA expression signatures in women using NGS

2019-01-11 | GSE124900 | GEO

Next Generation Sequencing (NGS) analysis of mice pancreatic islets from control and IMP2 islet specific knockout (Rip2;IMP2).

Project description:The goal of this study is to understand how IMP2 contributes to T2D traits by regulating pancreatic beta cell growth and function. Islets from control and Rip2;IMP2 mice were generated by deep sequencing. In additon, we also perfomred IMP2 RIP-Seq to identify IMP2 targets.

2023-06-11 | GSE152424 | GEO

N2O-reducing population in anaerobic digestate for next-generation biorest

Project description:Anaerobic digestion (AD) is a core technology in management of urban organic wastes, converting a fraction of the organic carbon to methane and the residual digestate, the biorest, have a great potential to become a major organic fertilizer for agricultural soils in the future. At the same time, mitigation of N2O-emissions from the agricultural soils is needed to reduce the climate forcing by food production. Our goal was therefore to enrich for N2O reducing bacteria in AD digestates prior to fertilization, and in this way provide an avenue for large-scale and low-cost cultivation of strongly N2O reducing bacteria which can be directly introduced to agricultural soils in large enough volumes to alter the fate of nitrogen in the soils. Gas kinetics and meta-omics (metagenomics and metaproteomics) analyses of the N2O enriched digestates identified populations of N2O respiring organisms that grew by harvesting fermentation intermediates of the methanogenic consortium.

2022-02-16 | PXD022030 | Pride

Next Generation Protein Sequencing

Project description:NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysis, de-novo long peptide tag sequencing of resulting peptides and assembly of peptide tags into consensus contigs.

2017-04-03 | PXD003804 | Pride

Gene expression between normal and cancer tissue for pancreatic cancer in Japan

Project description:Transcriptomic analysis of cancer samples helps to identify the mechanism and molecular markers of cancer. However, transcriptomic analyses of pancreatic ductal adenocarcinoma from the Japanese population are lacking. We performed RNA sequencing of flesh or frozen pancreatic ductal adenocarcinoma tissues and adjacent normal pancreatic tissue from 12 Japanese patients to identify genes critical for the clinical pathology of pancreatic cancer among the Japanese population.

2022-02-09 | GSE196009 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of CAFR and CAFS Transcriptomes in pancreatic cancer

Project description:We extracted primary CAFs from the tumor tissue of chemoresistant and chemosensitive pancreatic cancer patients (namely CAFR and CAFS). The Goal of this study is to compare the transcriptomes difference between CAFR and CAFS. And we come to a conclusion that CAFR is possessed of a iCAF phenotype.

2022-01-06 | GSE192907 | GEO

Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping

Project description:Host-pathogen interactions (HPIs) are pivotal in regulating establishment, progression, and outcome of an infection. Affinity-purification mass spectrometry has become instrumental for the characterization of HPIs, however the targeted nature of exogenously expressing individual viral proteins has limited its utility to the analysis of relatively small pathogens. Here we present the use of co-fractionation mass spectrometry (SEC-MS) for the high-throughput analysis of HPIs from native viral infections of two Jumbophages (phiKZ and phiPA3) in Pseudomonas aeruginosa. This enabled the detection >6000 unique host-pathogen and >200 pathogen-pathogen interactions for each phage, encompassing >50% of the phage proteome. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. Prediction of novel ORFs revealed a phiPA3 complex showing strong structural and sequence similarity to phiKZ nvRNAp, suggesting phiPA3 also possesses two RNA polymerases acting at different stages of the infection cycle. We further expanded our understanding on the molecular organization of the virion packaged and injected proteome by identifying 23 novel virion components and 5 novel injected proteins, as well as providing the first evidence for interactions between KZ-like phage proteins and the host ribosome. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction (https://phagemap.ucsf.edu/). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of hostpathogen interactomes and protein complex dynamics upon infection.

2023-04-14 | MSV000091715 | MassIVE

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