GEO DataSets

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) 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

(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) 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) 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) 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) 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) 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) Oesophageal exposure to duodenogastroesophageal refluxate is implicated in the development of Barrett’s Metaplasia, with increased risk of progression to oesophageal adenocarcinoma. The literature proposes that reflux exposure activates NF-kB, driving the aberrant expression of intestine-specific caudal-related homeobox genes. However, early events in the pathogenesis of Barrett’s Metaplasia from a normal epithelium are poorly understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

8 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling was performed using the total RNA isolated from pooled esophagi (plural of esophagus) of embryonic day 15.5 (E15.5) C57BL/6 mouse embryos and total RNA isolated from pooled esophagi of postnatal day 2 (P2) C57BL/6 pups. The goal was to identify differentially regulated genes in these two separate developmental stages.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2872

1 Sample

Download data: TXT

(Submitter supplied) Cdx2 has been suggested to play an important role in Barrett's esophagus (BE), or intestinal metaplasia (IM) in the esophagus. However, in vivo data have been lacking. The aim of the present study was to investigate whether transgenic overexpression of zCdx1b, the functional equivalent of mammalian Cdx2 in zebrafish, may lead to IM of squamous epithelium in zebrafish A transgenic zebrafish system was developed by expressing zCdx1b gene under the control of zebrafish keratin 5 promoter (zK5p). more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

5 Samples

Download data: CEL

(Submitter supplied) The forkhead box (FOX) family of transcriptional regulators is characterized by a distinct forkhead DNA-binding domain11. FOXF1 gene is highly conserved across species and implicated in embryonic digestive tract morphogenesis. In an in-vitro established model, normal esophageal squamous cells, EPC2, were transfected with FOXF1 to determine pathways regulated by FOXF1 during the squamous to columnar change in cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

26 Samples

Download data: TXT

(Submitter supplied) Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) To test the hypothesis that there are specific miRNA/UCR expression signature which characterizes Barrett's esophagus development and progression, we performed miRNA/UCR microarray analysis comparing normal esophageal squamous epithelium with all the phenotypic lesions seen in the Barrett's carcinogenic process

Organism:

Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL8871

51 Samples

Download data: GPR

(Submitter supplied) Cdx2/IL-1beta mice have less intestinal metaplasia at the squamocolumnar junction thanIL-1beta mice alone. This study was to identify a mechanism for this effect by examining differences in gene expression patterns when Cdx2 is co-expressed.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL, XLSX