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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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

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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

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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 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 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

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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

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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

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

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