Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gastric Mutational Signatures GMS

ABSTRACT: This study aims to characterise the mutation burdens and signatures of adult stem cells derived from different regions of the stomach in order to gain insight into the causes and preclinical evolution of the diverse cancer subtypes. Clonal populations of cells from different anatomical locations of the stomach will be derived through organoid culture and/or laser microdissection and interrogated by whole genome sequencing and/or targeted pulldown. A total of circa 300 samples from 20 Â– 30 donors (cancer and non-cancer patients undergoing total/partial gastrectomy) will be analysed for mutational burden and signatures and genomic findings correlated with topology, age, risk factors and different stages of pre-neoplastic or neoplastic progression.

PROVIDER: EGAS00001002939 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Gastric Mutational Signatures GMS

Project description:This study aims to characterise the mutation burdens and signatures of adult stem cells derived from different regions of the stomach in order to gain insight into the causes and preclinical evolution of the diverse cancer subtypes. Clonal populations of cells from different anatomical locations of the stomach will be derived through organoid culture and/or laser microdissection and interrogated by whole genome sequencing and/or targeted pulldown. A total of circa 300 samples from 20 Â– 30 donors (cancer and non-cancer patients undergoing total/partial gastrectomy) will be analysed for mutational burden and signatures and genomic findings correlated with topology, age, risk factors and different stages of pre-neoplastic or neoplastic progression.

| EGAS00001002938 | EGA

The proteomic and transcriptomic profiles of gastric mucosa from health volunteers

Project description:As the important layer of the stomach wall, gastric mucosa is related to many functions of digestion. According to the anatomical location, the human stomach is divided into seven regions. In order to get an entire profiling of the 7 regions at proteomic and transcriptomic levels, we collected 7 biopsies from each health volunteer, 49 total were used for integrative analysis, and measured the regional-specific gene products to define the reference intervals of gene expression for outliers screening and prognostic gene detection. Collectively, we presented profiling of normal gastric mucosa at different levels and defined reference ranges of gene expression to study the specific characteristics of abnormal and cancer samples, providing a better understanding of stomach physiological function in studies of gastric disease mechanism.

2024-04-01 | GSE250499 | GEO

RNAi of signal transduction components in HCT116 cells

Project description:We performed RNAi knockdown experiments on 7 different signal transduction components of the Wnt pathway in HCT116 colon cancer cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract common pathway signatures and enabeling us to perform susequent nested effects modelling. the resulting pathway models yields new insight in the pathway topology in colon cancer.

2014-04-18 | E-MTAB-651 | biostudies-arrayexpress

Gene expression prfile of ARID1A knockout N87 cells

Project description:To identify ARID1A-regulated genes in stomach cancer, we performed microarray profiling of RNA isolated from N87 stomach cancer cells, in which ARID1A expression was knocked down by two different siRNAs against ARID1A.

2019-05-14 | GSE118273 | GEO

Proteomic profiling of KIT-containing EVs secreted by neoplastic human mast cells (SUB1)

Project description:Activating mutations in the receptor KIT promote the dysregulated proliferation of human mast cells (huMCs). The resulting neoplastic huMCs secrete extracellular vesicles (EVs) that can transfer oncogenic KIT among other cargo into recipient cells. Despite potential contributions to diseases, KIT-containing EVs have not been thoroughly investigated. Here, we isolated KIT-EV subpopulations released by neoplastic huMCs using an immunocapture approach that selectively isolates EVs containing KIT in its proper topology. Proteomic profiling was performed on KIT-containing EVs compared to KIT-depleted EV populations, and on KIT-EVs that are microvesicle- and exosome-like.

2023-03-10 | PXD033889 | Pride

Gene expression profiling of gastroesophageal adenocarcinoma

Project description:We aimed to genetically characterize adenocarcinomas in the gastroesophagel junction in relation to cancers in the esophagus and the stomach. In total 27 tumors was genetically profiled using gene expression array. Adenocarcinomas located in the gastroesophageal junction showed strong similarites with tumors in the distal esophagus, whereas different profiles were generated for tumors in the proximal stomach.

2010-05-29 | GSE22050 | GEO

Laser Capture Microdissection Provides a Novel Molecular Profile of Human Primary Cutaneous Melanoma

Project description:Melanoma accounts for the majority of skin cancer related mortality. In-depth molecular analysis of neoplastic melanocytes in whole tissue biopsies is diluted by the inflammatory infiltration, which may obscure gene signatures specific to neoplastic cells. Thus, a method is needed to precisely uncover molecular changes specific to tumor cells from a limited sample of primary melanomas.

2024-02-14 | GSE238207 | GEO

STAD_ZGYXKXYZLYY_20190816_WGS

Project description:stomach cancer

| OEX00013357 | NODE

STAD_BJDXZLYY_Protein

Project description:stomach cancer

| OEX00013358 | NODE

Construction and Application of an Epigenetic Atlas of the Human Heart

Project description:Epigenetic modifications including DNA methylation regulate gene expression and contribute to specialization of cells. Currently, there is limited knowledge of the epigenetic patterns of human heart. We have used healthy cardiac tissues from different anatomical regions of the human heart to study unique methylation signatures specific to human heart.

2020-03-04 | GSE146297 | GEO

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