Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human esophageal cancer samples

ABSTRACT: To compare gene expression profiles between normal, Barrett's Esophagus, ADC and SCC samples.

INSTRUMENT(S): Scanning hardware

ORGANISM(S): Homo sapiens

DISEASE(S): normal

SUBMITTER: Wayne Phillips

PROVIDER: E-MEXP-692 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Non-endoscopic screening biomarkers for Barrett's oesophagus: from microarray analysis to the clinic.

Lao-Sirieix P P Boussioutas A A Kadri S R SR O'Donovan M M Debiram I I Das M M Harihar L L Fitzgerald R C RC

Gut 20090802 11

<h4>Background and aims</h4>Barrett's oesophagus predisposes to oesophageal adenocarcinoma but the majority of patients are undiagnosed. A novel non-endoscopic cytological screening device, called a capsule sponge, makes population-based screening for the disease a feasible option. However, due to the mixed cell population retrieved by the capsule sponge, biomarkers specific for Barrett's oesophagus are required.<h4>Methods</h4>Three publically available microarray datasets were used to identify ...[more]

PMID: 19651633

Similar Datasets

Transcription profiling of human squamous cell carcinomas to predict response to neoadjuvant chemoradiotherapy in oesophageal cancer patients

Project description:To use gene expression profiles to predict response to neoadjuvant chemoradiotherapy in oesophageal cancer patients.

2008-02-08 | E-MEXP-426 | biostudies-arrayexpress

Transcription profiling of human normal vs Barretts Oesophagus samples

Project description:To compare gene expression profiles between normal and Barrett's Oesophagus samples. <BR><BR>This experiment contains a partial data set. The full data set can be found in experiment E-MEXP-692.

2006-11-06 | E-MEXP-425 | biostudies-arrayexpress

Transcription profiling by array of human serum-free fibrocytes, serum-containing fibrocytes, CD14++CD16- Monocytes, CD14++CD16+ Monocytes, CD14+CD16++ Monocytes and macrophages

Project description:Serum-free Fibrocytes, Serum-containing Fibrocytes, CD14++CD16- Monocytes, CD14++CD16+ Monocytes, CD14+CD16++ Monocytes, Macrophages were all generated from up to 3 biological replicates from each of 3 separate donors. RNA was extracted (Ambion RNAqueous), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon). Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. Final data analysis was carried out using TMEV 4.0. SAM was performed using a 0.1% FDR. PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment.

2011-01-01 | E-MEXP-2811 | biostudies-arrayexpress

Transcription profiling of human CD4 regulatory T cells that express either CD45RA or CD45RO

Project description:CD4 T cells taken from 6 donors were sorted into CD25hi CD45RA+ (naï¿½ve Treg), CD25hi CD45RO+ (memory Treg), CD25- CD45RA+ (naï¿½ve responder) and CD25- CD45RO+ (memory responder) populations. <br><br>RNA was extracted (Ambion RNAqueous), amplified (SMART), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon).<br><br>Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. One sample was deemed to be of too low hybridisation quality, and was hence removed at this point.<br><br>Final data analysis was carried out using TMEV 4.0. SAM was performed using a 10% FDR. HCL and PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment<br>

2009-10-05 | E-MEXP-2372 | biostudies-arrayexpress

Transcription profiling of human distinct types of fibrocyte differentiate in the presence and abscence of serum

Project description:Fibroblasts, Serum-free Fibrocytes, Serum-containing Fibrocytes, Monocytes, Macrophages, Osteoclasts, immature Dendritic Cells, and mature Dendritic Cells were all generated from 3 biological replicates from each of 3 separate donors. RNA was extracted (Ambion RNAqueous), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon). Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. Final data analysis was carried out using TMEV 4.0. SAM was performed using a 0.1% FDR. HCL and PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment. After initial analysis, the Fibroblast cell type was found to significantly bias the data. Due to this, these samples were removed from the analysis, and the data re-normalised. This second data file will be submitted separately.

2010-04-29 | E-MEXP-2434 | biostudies-arrayexpress

Transcription profiling of Streptococcus mutans grown in a biofilm with or without the presence of Veillonella parvula

Project description:Streptococcus mutans was grown for 48 h in a biofilm in the absence (single species) and in the presence (dual species) of Veillonella parvula. In addition V. parvula single species 48 h biofilms were grown, to be used as a control. RNA was harvested from all types of biofilms and the transcript levels of the two types of biofilms containing S. mutans were compared with the use of S. mutans microarrays. V. parvula RNA was hybridized to S. mutans microarrays as a control for possible cross-hybridisation.

2007-06-14 | E-MEXP-1034 | biostudies-arrayexpress

Transcription profiling of mouse ATCC CRL1606 hybridoma cells to evaluate microarray gene identification methods using spike-in experiments

Project description:Due to the lack of controlled microarray experimental data, evaluation of gene identification methods has been performed using simulated/manipulated data. As the ability of these approaches to mimic actual experimental data is questionable, conclusions drawn can be misleading. We applied spike-in approaches to develop experimental benchmark data and used it to evaluate various gene identification methods. <br> <br> mRNA was obtained from mouse ATCC CRL1606 hybridoma cells. From self hybridization results 200 genes that consistently exhibited a log ratio value close to 0 were randomly selected across a range of intensity. In-vitro transcripts of these 200 genes were obtained from their respective clones. From RNA gel electrophoresis and test array results, 169 of the 200 transcripts were deemed successful. Experiments were then conducted by spiking these 169 transcripts to the common pool of mRNA extracted from the hybridoma cells. With exception of the spiked in genes, the experimental set-up is identical to a self hybridization. This experiment is thus different from other microarray experiments as the set of differentially expressed genes is known as they have been artificially created. <br> <br> <br>

2005-03-17 | E-MEXP-280 | biostudies-arrayexpress

Transcription profiling of human fibroblast RNA from patient with a mitochondrial oxidative phosphorylation complex I deficency vs normal fibroblast RNA

Project description:Comparison of fibroblast RNA from patient with a mitochondrial oxidative phosphorylation complex I deficency to normal fibroblast RNA.<br><br>Note: this experiment submission is not fully MIAME compliant, due to the unavailability of oligonucleotide sequences on the A-MEXP-70 array ("Adelaide, H.sapiens, 19k array, version 1").

2004-09-01 | E-MEXP-118 | biostudies-arrayexpress

Transcription profiling of human fibroblast RNA from a patient with a mitochondrial oxidative phosphorylation complex I deficiency vs normal fibroblast RNA

Project description:Comparison of fibroblast RNA from a patient with a mitochondrial oxidative phosphorylation comnplex I deficiency against normal fibroblast RNA.<br><br>Note: this experiment submission is not fully MIAME compliant, due to the unavailability of oligonucleotide sequences on the A-MEXP-70 array ("Adelaide, H.sapiens, 19k array, version 1").

2004-09-01 | E-MEXP-119 | biostudies-arrayexpress

Transcription profiling of wild type, sco1 and sco2 knock out mutants of S. cerevisiae BY4741 in early response to different doses of oleic acid

Project description:This experiment describes the transcriptional response to oleic acid as a sole carbon source of yeast strains differing in their respiratory competence: the BY4741 wild type strain is considered as normal, sco1 knock out mutant is respiratory deficient and sco2 knock out mutant has a better respiratory competence then the wild type strain. The three strains underwent metabolic shift from 2% glucose as a carbon source to oleic acid at both standard (0.1%) and high (5%) concentration. The transcriptional profiling comprises two time points after metabolic shift: 2 hours and 5 hours. mRNA levels were compared with reference growth condition: exponential phase in 2% glucose. The purpose of this experiment is to gain deeper insight in the relationship between fatty acid metabolism and respiratory metabolism.

2011-01-31 | E-TABM-614 | biostudies-arrayexpress

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