Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic lineage analysis in intramucosal gland-forming gastric neoplasms

ABSTRACT: To predict the progression risk of non-invasive gland-forming gastric neoplasms to invasive carcinoma, we assessed lineage continuity or discontinuity between the non-invasive and invasive neoplasms by applying hierarchical clustering analysis to the gene copy-number profiles of individual tumours. array-based Comparative Genomic Hybridization. Samples are including of 7 tumours of Vienna category 3, 12 tumours of Vienna category 4, 8 intramucosal cancers (Vienna category 5), 16 intramucosal lesions and 16 invasive parts (Vienna category 5); 40 reference for control, 19 control replicates

ORGANISM(S): Homo sapiens

SUBMITTER: Takahisa Nakayama

PROVIDER: E-GEOD-60116 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genomic profiling of gastric adenomas by array-based comparative genomic hybridization

2010-02-01 | GSE19574 | GEO

Genomic profiling of gastric carcinoma in situ by array-based comparative genomic hybridization

2010-02-01 | GSE19566 | GEO

Genomic profiling of gastric carcinoma in situ by array-based comparative genomic hybridization

Project description:In this study, we investigated CNAs of 20 gastric CIS (Vienna category 4.2) and 20 adenomas, including 7 low-grade adenomas (LGA; Vienna category 3) and 13 high-grade adenomas (HGA; Vienna category 4.1), by 244k oligonucleotide-based array comparative genomic hybridization (array CGH). 20 gastric carcinoma in situ (CIS) vs. 20 controls. The supplementary file 'GSE19566_aberrations.txt' file contains a summary of the aberrations in the gastric CISs as determined by the ADM-2 algorithm.

2010-01-31 | E-GEOD-19566 | biostudies-arrayexpress

Genomic profiling of gastric adenomas by array-based comparative genomic hybridization

Project description:In this study, we investigated CNAs of 20 gastric CIS (Vienna category 4.2) and 20 adenomas, including 7 low-grade adenomas (LGA; Vienna category 3) and 13 high-grade adenomas (HGA; Vienna category 4.1), by 244k oligonucleotide-based array comparative genomic hybridization (array CGH). 20 gastric adenomas vs. 20 controls. The supplementary file 'GSE19574_aberrations.txt' file contains a summary of the aberrations in the gastric adenomas as determined by the ADM-2 algorithm.

2010-06-18 | E-GEOD-19574 | biostudies-arrayexpress

Genetic lineage analysis in intramucosal gland-forming gastric neoplasms

Project description:To predict the progression risk of non-invasive gland-forming gastric neoplasms to invasive carcinoma, we assessed lineage continuity or discontinuity between the non-invasive and invasive neoplasms by applying hierarchical clustering analysis to the gene copy-number profiles of individual tumours.

2014-08-06 | GSE60116 | GEO

Quantitative Proteomic Profiling for Predicting Grade of Dysplasia in Intraductal Papillary Mucinous Neoplasm using Pancreatic Cyst Fluid

Project description:The increased number of pancreatic cyst lesions (PCLs) have been detected through the development of abdominal imaging techniques, such as computed tomography (CT), magnetic resonance imaging (MRI), and endoscopic ultrasound (EUS). However, accurate classification of cystic lesions is difficult because of the lack of standardized diagnostic methods, and thus potentially unnecessary surgical resection has been performed on pancreatic cyst patients. Among four most common types of cystic lesions of pancreas, intraductal papillary mucinous neoplasms (IPMNs), mucinous cystic neoplasms (MCN), serous cystic neoplasms (SCN), and solid pseudopapillary neoplasms (SPNs), IPMNs, the precursor lesion of pancreatic cancer, have been detected most frequently, and are subdivided into low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive IPMN in accordance with their malignancy. To discover the potential biomarkers of the histological grades of IPMN, we investigated pancreatic cyst fluid proteins that are differentially expressed in accordance with the IPMN malignancy by LC-MS/MS analysis.

2020-09-06 | PXD016127 | Pride

Quantitative Proteomic Analysis of Pancreatic Cyst Fluid Proteins Associated with Malignancy in Intraductal Papillary Mucinous Neoplasms

Project description:Intraductal papillary mucinous neoplasm (IPMN) is a benign tumor that grows within the pancreatic ducts characterized by the production of thick mucinous fluid by surrounding tumor cells. IPMN is the most important precursor lesion for pancreatic cancer that is the fourth most common cause of cancer deaths. Differentiating between low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive intraductal papillary mucinous neoplasms (IPMNs) remains a diagnostic challenge with current biomarkers, necessitating the development of novel biomarkers that can distinguish IPMN malignancy. We investigated differentially expressed proteins among pancreatic cyst fluids consisted of LGD, HGD, and invasive IPMN patients by using our novel proteomic strategy, and finally we discovered pancreatic cyst fluid protein marker candidates that can predict the malignant potential of IPMNs.

2018-05-01 | PXD008302 | Pride

U87_Radio_Resistance_Invasive_Noninvasive

Project description:Background: Glioblastoma multiforme (GBM) is the most common and malignant primary brain tumor in adults. Radiotherapy is together with surgery the mainstay treatment in management of patients with GBM, however, infiltrative growth pattern and radioresistance of glioma cells impedes therapeutic effects. Our study sought to investigate 1) whether GBM invasive cells render them resistant to radiotherapy and 2) what are the potential molecular mechanisms underlying the radioresistance via gene expression profiling. <br>Procedures: In-vitro selection of invasive cells using matrigel-coated transwell assay: U87 cells were starved 8h prior to seeding. 5x105 cells in 2 mL serum-free DMEM medium were plated in the upper transwell inserts of a 6-well Boydem chamber. 10% FCS was added in the medium of the lower chamber. After 20h incubation, non-invasive cells on the surface of the membrane were scratched and recovered. Invasive cells migrating through matrigel due to the gradient of attractant were recovered by trypsin/EDTA after the membrane was washed with PBS twice and swabbed by cotton tips. Evaluate the invasiveness of selected phenotype of U87 cells by time-lapse wound-healing assay: 5x104 cells in 100μL serum-free DMEM medium were seeded in a 96-well ImageLock plate with each well was pre-coated with matrigel. Wounds were scratched using a 96-pin WoundMaker and gently washed with 2xPBS. After cooling equilibration, the wounds were coated with a second layer of matrigel. The microplate was incubated at 37oC and 5% CO2 for 30min. Cell invasion was recorded by living-image microscopy over 48h. Microarray: after confirmation of enhanced invasive ability, invasive and non-invasive cell populations were used for RNA isolation, cDNA transcription, and chip hybridization.

2023-11-08 | E-MTAB-4608 | biostudies-arrayexpress

Genotyping of human lung cancer cells on the 10K Affymetrix SNP array to validate whole genome amplification of genomic DNA from laser captured microdissectates and genotyping serial samples of developing lung cancers to identify early events

Project description:A series of experiments were performed to validate whole genome amplification of genomic DNA from laser captured microdissectates and the technique was then applied to serial samples of developing lung cancers to identify early events. 10K Affymetrix SNP arrays were used.

2006-10-01 | E-TABM-134 | biostudies-arrayexpress

Predicting the evolution of metastatic disease in breast cancer: results from 50 years of autopsies

Project description:This is a genomic analysis of breast cancer metastasis using array based CGH and is part of a large study investigating the patterns and evolution of metastases from breast cancer using autopsy material accumulated over the last 50 years from a single institution. The samples used in the genomic profiling comprise the primary breast tumour and multiple matched metastases from each patient. The data demonstrate both the clonal nature of metastatic progression and the role of clonal evolution during progression. This study comprises six patients who died of metastatic breast cancer. For some patients the breast primary tumour and lymph node metastasis was obtained from previous surgical excision, otherwise material was obtained from a resulting autopsy. Each patient set of samples involves the primary breast tumour and multiple metastases, including from lung, liver, lymph node, adrenal gland, brain etc. DNA was extracted from formalin fixed paraffin embedded (FFPE) tissue blocks and analysed for DNA copy number alterations using an Agilent aCGH platform.

2013-11-11 | E-GEOD-46826 | biostudies-arrayexpress

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