GEO DataSets

(Submitter supplied) Samples were obtained from 8 patients with Barrett's associated adenocarcinomas after transhiatal esophagectomy. Samples representative of the normal esophageal epithelium (N), Barrett’s esophagus (B) and esophageal adenocarcinomas (ADC) were obtained from every patient by experienced GI pathologists. RNA were extracted and samples were profiled for detection of genes differentially expressed in B and ADC relative to N and in ADC relative to B. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1321

Platform:

GPL96

24 Samples

Download data: CEL

Expression profiling of normal esophageal epithelium, premalignant Barrett's metaplasia, and esophageal adenocarcinoma samples. Tissue samples of each type obtained from 8 patients by transhiatal esophagectomy. Results identify potential markers of disease progression.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state, 8 individual sets

Platform:

GPL96

Series:

GSE1420

24 Samples

Download data: CEL

(Submitter supplied) Patients were recruited at the Departments of Abdominal Surgery and Endoscopy of the Hospital do Cancer AC Camargo (São Paulo/Brazil) during a 4-year period (2001 to 2004). All patients signed a pre-informed consent and the study was approved by the internal ethics committee. Tissue samples were either snap frozen in liquid nitrogen (when obtained by surgery) or collected in RNAlaterTM (Ambion®, Austin, Texas USA, when obtained by biopsy). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1930

172 Samples

Download data

(Submitter supplied) Spotted cDNA Orestes clones. This set includes 4608 orestes in build 175 of the human UniGene database. Keywords = spotted, cDNA

Organism:

Homo sapiens

13 Series

1103 Samples

Download data

(Submitter supplied) samples contain normal, Barrett and duodenum and adenocarcinoma BACKGROUND & AIMS: Barrett's esophagus is a precursor of esophageal adenocarcinoma. DNA microarrays that enable a genome-wide assessment of gene expression enhance the identification of specific genes as well as gene expression patterns that are expressed by Barrett's esophagus and adenocarcinoma compared with normal tissues. Barrett's esophagus length has also been identified as a risk factor for progression to adenocarcinoma, but whether there are intrinsic biological differences between short-segment and long-segment Barrett's esophagus can be explored with microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

48 Samples

Download data

(Submitter supplied) Goal of the microarray study is to identify 2-fold or more differentially expressed genes common to all three "tumor vs. normal" dye-swap pairs. Keywords: repeat sample

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS2229

Platform:

GPL1415

6 Samples

Download data: TIFF

Analysis of three rodent carcinoma cell lines established from two biliary reflux-associated tumors. Gastroesophageal reflux disease is associated with the development of esophageal adenocarcinoma. Results identify upregulation of several cancer-related genes important in human esophageal cancer.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, log2 ratio, 3 cell line sets

Platform:

GPL1415

Series:

GSE1707

6 Samples

Download data: TIFF

(Submitter supplied) Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that frequently develops from Barrett’s esophagus (BE), a premalignant pathological change occurring in the lower end of esophagus. To identify BE patients at high risk of malignant transformation is essential to the prevention of EAC. Although microRNA (miRNA) expression signatures have been associated with the etiology and prognosis of several types of cancers, their roles in the development of EAC have not been extensively evaluated.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL6955

32 Samples

Download data: TXT

(Submitter supplied) mucosal biopsies were taken from patients at pre and post-argon plasma coagulation (APC) ablation of Barrett's oesophagus, and from healthy controls. Total RNA was extracted using Trizol. miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a high throughput TaqMan® OpenArray® Human microRNA panel (Life technologies, #4461104). more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL17485

57 Samples

Download data: TXT

(Submitter supplied) To begin to identify genes involved in the transdifferentiation process we analyzed Barrett’s esophagus (with no dysplasia), normal esophagus and small intestine biopsy samples by Affymetrix microarray. Keywords: microarray expression analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3472

Platform:

GPL96

19 Samples

Download data: CEL

Analysis of Barrett's esophagus (BE), normal esophageal, and small intestinal biopsies. In BE, normal esophageal squamous epithelium transdifferentiates into simple columnar epithelium resembling that of small intestine. Results provide insight into the molecular basis of this transdifferentiation.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state, 8 individual, 2 tissue sets

Platform:

GPL96

Series:

GSE13083

19 Samples

Download data: CEL

(Submitter supplied) Esophageal adenocarcinoma (EAC) has become a major concern in Western countries due to rapid rises in incidence coupled with very poor survival rates. One of the key risk factors for the development of this cancer is the presence of Barrett’s esophagus (BE), which is believed to form in response to repeated gastro-esophageal reflux. In this study we performed comparative, genome-wide expression profiling (using Illumina whole-genome Beadarray) on total RNA extracted from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC) and those with normal squamous epithelium. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2507

54 Samples

Download data: TXT

(Submitter supplied) Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis. We performed genomic location analysis of the pioneer transcription factor FoxA in the adult liver and found that about one-third of the FoxA bound sites are near silent genes, including genes without detectable RNA polymerase II. Virtually all of the FoxA-bound silent sites are within extended conserved sequences, suggesting possible function. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10774

3 Samples

Download data: TXT

(Submitter supplied) Barrett's esophagus is characterized by the replacement of squamous epithelium with specialized intestinal metaplastic mucosa. The exact mechanisms of initiation and development of Barrett's metaplasia remain unknown, but a hypothesis of successful adaptation against noxious reflux components has been proposed. To search for the repertoire of adaptation mechanisms of Barrett's metaplasia, we employed high-throughput functional genomic and proteomic methods that defined the molecular background of metaplastic mucosa resistance to reflux. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

46 Samples

Download data: CEL

(Submitter supplied) A nonsense mutation in ARID1A was identified by next generation sequencing in non-dysplastic Barrett's esophagus [BE] tissue and esophageal adenocarcinoma [EAC] tissue of a patient diagnosed with EAC. Immunohistochemistry performed on an independent archival cohort demonstrated ARID1A protein loss in 0% (0/76), 4.9% (2/40), 14.3% (4/28), 16.0% (8/50), and 12.2% (12/98) of normal squamous epithelium, BE, low-, high-grade dysplasia, and EAC tissues, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

4 Samples

Download data: CEL

(Submitter supplied) Signal transducer and activator of transcription 3 (STAT3) is altered in several epithelial cancers and represents a potential therapeutic target. Here, STAT3 expression, activity and cellular functions were examined in two main histotypes of esophageal carcinomas. In situ, immunohistochemistry for STAT3 and STAT3-Tyr705 phosphorylation (P-STAT3) in esophageal squamous cell carcinomas (ESCC) and Barrett’s adenocarcinomas (BAC) revealed similar STAT3 expression in ESCCs and BACs, but preferentially activated P-STAT3 in ESCCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) miR-223 is step-wise increasingly up-regulated in the normal esophagus - Barrett's esophagus -esophageal adenocarcinoma carcinoma sequence. In this study, we aimed to determine the function of miR-223 in esophageal adenocarcinoma carcinogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

4 Samples

Download data: TXT

(Submitter supplied) Our mouse model of BE in which overexpression of IL-1b in the squamous esophagus induces chronic inflammation leads to metaplasia and dysplasia at the squamo-columnar junction (SCJ) in the mouse gastro-esophageal junction resembles the human disease. Adult L2-IL1b mice were employed to investigate changes to the transcriptional landscape at the SCJ during disease progression from BE to EAC following pharmaceutical or genetic perturbations of interest to BE biology.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

48 Samples

Download data: CEL

(Submitter supplied) This study utilise the examination of normal gastro-intestinal tissues to determine a tissue specific signal for use in deriving the intestinal signature of intestinal metaplasias of the oesophagus. Normal oesophageal, colonic and duodenal tissue biopsies were taken after informed consent and RNA was extracted following histological examination of adjacent tissues for normal aperaing mucosa.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL

(Submitter supplied) Our analysis reveals an extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

160 Samples

Download data: CSV