Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oesophageal cancer neo-adjuvant

ABSTRACT: Oesophageal adenocarcinoma exome sequence data from samples before and after neo-adjuvant chemotherapy

PROVIDER: PRJEB12657 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1345880_1.fastq.gz	Fastqsanger.gz
	ERR1345880_2.fastq.gz	Fastqsanger.gz
	ERR1345890_1.fastq.gz	Fastqsanger.gz
	ERR1345890_2.fastq.gz	Fastqsanger.gz
	ERR1345900_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 264

Similar Datasets

Gene expression profiling of 60 pre-chemotherapy FFPE endoscopic oesophageal adenocarcinoma biopsies

Project description:Oesophageal cancer is the ninth most common cancer in the UK and accounts for 5% of all cancer deaths. The incidence of the disease in men has risen 50% in the last 25 years with the commonest pathological subtype in the West being adenocarcinoma, while in East Asia oesophageal squamous cell carcinoma predominates. Despite efforts to screen for Barrett’s oesophagus, and pre-operatively select OAC patients who are likely to benefit from potentially curative surgery, survival remains poor. The five year survival rate is less than 17% and even in early stage locoregional confined disease this figure lies between 25-35%. A significant improvement in overall survival has been demonstrated with neo-adjuvant or peri-operative chemotherapy but the optimal approach for individual patients remains unclear. A consistent finding has been that complete histopathological response to neo-adjuvant chemotherapy is a prognostic biomarker for increased survival benefit. Therefore, there is a pressing need to identify biomarkers capable of predicting response, enabling clinicians to select patients for whom neo-adjuvant therapies would be beneficial. This experiment represents gene expression profiling of 60 pre-treatment formalin-fixed paraffin embedded (FFPE) oesophageal adenocarcinoma biopsies. All patients were treated with neo-adjuvant cisplatin-based chemotherapy prior to surgical resection at the Northern Ireland Cancer Centre from 2004-2012. The aim of the experiment was to carry out functional enrichment of pathological responders and non-responders to neo-adjuvant chemotherapy in order to identify novel mechanism of drug resistance or chemo-sensitivity.

2018-05-10 | E-MTAB-4666 | biostudies-arrayexpress

Gene Expression Profiling of FFPE Pre-treatment Endoscopic Biopsies from Oesophageal Adenocarcinoma Patients Treated with Neo-adjuvant Chemotherapy and Surgical Resection

Project description:Gene expression profiling of 273 pre-treatment endoscopic FFPE oesophageal and oesophago-gastric junctional adenocarcinomas for validation of a DNA Damage Response Deficiency Assay. All patients were treated with neo-adjuvant chemotherapy followed by surgical resection and were collected at four UK centres in the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium between 2004 and 2013. Biopsies were reviewed for pathological subtype prior to marking for macrodissection and samples containing at least 50% adenocarcinoma tissue by area were taken forward. Total RNA was extracted using the RecoverallTM Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, Waltham, MA) and amplified using the NuGen Ovation FFPE Amplification System v3 (NuGen San Carlos, CA). The amplified product was hybridized to the Almac Diagnostics Xcel™ array (Almac, Craigavon, United Kingdom), a cDNA microarray-based technology optimized for archival FFPE tissue, and analysed using the Affymetrix 7G scanner (Affymetrix, Santa Clara, CA)

2019-01-31 | E-MTAB-6969 | biostudies-arrayexpress

Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS

Project description:Oesophageal adenocarcinoma (OAC) is an aggressive cancer with a five-year survival of <15%, and the incidence is predicted to double within the next 20 years. Current neo-adjuvant chemotherapy treatment strategies only benefit a minority (20-30%) of patients and there are currently no methods available to differentiate between responders and non-responders. Here we performed quantitative proteomics using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) on albumin/IgG-depleted and non-depleted plasma samples from 23 patients with locally advanced OAC or oesophageal gastric junction cancers prior to treatment. Individuals were grouped based on tumour regression (TRG) score (TRG1-3 vs TRG4 and 5) after chemotherapy and differentially abundant proteins were compared using univariate and multivariate analyses. Protein depletion led to the identification of around twice as many proteins in the samples compared to non-depletion. SWATH-MS revealed significant quantitative differences in the abundance of several proteins (p<0.05) between the two groups. These included all three c1q subunit proteins, C1QA, C1QB and C1QC, which were of higher abundance in the low TRG group (higher degree of regression in response to treatment). Of those that were found to be of higher abundance in the high TRG group, GSTP1 was found to exhibit the lowest p-value (univariate analysis) and highest accuracy and Cohen’s kappa value (multivariate analysis). The concentrations of c1q complex and GSTP1 were further examined and validated using ELISA-based assays. This study provides quantitative information relating to differences in the plasma proteome that underpin response to chemotherapeutic treatment in oesophageal cancers.

2022-08-22 | PXD032137 | Pride

miRNA profiling of longitudinal ovarian cancer biopsies collected before and after platinum-based neo-adjuvant chemotherapy

Project description:In the last decades platinum-based neo-adjuvant chemotherapy (NACT) has been recognized as a reliable therapeutic strategy in patients with un-resectable advanced epithelial ovarian cancer (EOC). However, the molecular changes induced by NACT at miRNA level, and their prognostic role has not been clarified until now. In order to uncover miRNAs that are altered in EOC tumor which received NACT, we performed whole-miRNA analysis on 82 FIGO Stage IIIC-IV high-grade serous (HGS) tumors, whose samples had been collected at complete primary debulking (PDS) and at interval-debulking surgery (IDS) after fter 4 courses of NACT.

2016-01-20 | E-MTAB-3696 | biostudies-arrayexpress

Gene induction by low pH in oesophageal cells

Project description:Differential gene expression analysis of oesophageal cells stimulated with a low pH environment. Study designed to identify pathways involved in progression of gastro-oesophageal reflux disease through Barrett's oesophagus to adenocarcinoma. Identified many subsets of genes with involvement in pathogenesis. Keywords = GORD Keywords = Barrett's Oesophagus Keywords = Oesopageal Adenocarcinoma. Keywords: time-course

2005-10-04 | GSE2144 | GEO

RNAseq of Oesophageal Adenocarcinoma Cell Lines

Project description:rna sequencing of Oesophageal Adenocarcinoma Cell lines: OACP4, OE19, FLO-1, SK-GT-4, ESO26, OE33, ESO51, OACM5.1 C, JH-EsoAd1

2022-06-01 | GSE153096 | GEO

Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment

Project description:Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment

| PRJNA613650 | ENA

Oesophageal adenocarcinoma global proteomes

Project description:We present data of global proteomes for oesophageal adenocarcinoma and for normal adjacent tissue from seven donors.

2024-12-17 | PXD054428 | Pride

Identification of novel molecular subgroups in esophageal adenocarcinoma to predict response to neo-adjuvant therapies

Project description:Identification of novel molecular subgroups in esophageal adenocarcinoma to predict response to neo-adjuvant therapies

| PRJNA855976 | ENA

A Study of the Gene Expression of Colorectal Liver Metastases: Tumour, ‘Halo’ and Liver Parenchyma

Project description:This was a study comparing the gene expression of liver parenchyma, metastatic colorectal cancer within the liver, and the halo, which is an artifactual area which contained metastatic colorectal cancer before neo-adjuvant chemotherapy reduced the cancer.

2020-05-01 | GSE38174 | 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