Copy number variation analysis of human Barrett's esophagus stem cells
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ABSTRACT:
PROVIDER: PRJNA283319 | ENA |
REPOSITORIES: ENA
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Project description:Barrettâs esophagus confers significant risk of esophageal adenocarcinoma. We have established the cloning system of patient-matched stem cells of Barrettâs esophagus and gastric cardia. Barrett's esophagus (BE) stem cells and gastric cardia (GC) stem cells from 12 patients were cloned. To analyze copy number variation in BE and GC stem cells, we have performed SNP array. It has shown that deletions such as p16 and FHIT in BE stem cells are significantly detected, while amplifications in BE stem cells are not. Also, we found some of BE stem cells did not share these deletions, suggesting emerging of BE does not require specific CNV. SNP array based copy number variation study was performed for BE and GC stem cells from human endoscopic biopsy (12 patients) to assess genomic stability at chromosomal level.
2016-01-13 | E-GEOD-68663 | biostudies-arrayexpress
Project description:Barrett’s esophagus confers significant risk of esophageal adenocarcinoma. We have established the cloning system of patient-matched stem cells of Barrett’s esophagus and gastric cardia. Barrett's esophagus (BE) stem cells and gastric cardia (GC) stem cells from 12 patients were cloned. To analyze copy number variation in BE and GC stem cells, we have performed SNP array. It has shown that deletions such as p16 and FHIT in BE stem cells are significantly detected, while amplifications in BE stem cells are not. Also, we found some of BE stem cells did not share these deletions, suggesting emerging of BE does not require specific CNV.
2016-01-13 | GSE68663 | GEO
Project description:Barrett’s esophagus confers significant risk of esophageal adenocarcinoma. We have established the cloning system of patient-matched stem cells of Barrett’s esophagus and gastric cardia. Barrett's esophagus (BE) stem cells and gastric cardia (GC) stem cells from 12 patients were cloned. To analyze copy number variation in BE and GC stem cells, we have performed SNP array. It has shown that deletions such as p16 and FHIT in BE stem cells are significantly detected, while amplifications in BE stem cells are not. Also, we found some of BE stem cells did not share these deletions, suggesting emerging of BE does not require specific CNV.
2016-01-13 | GSE68662 | GEO
Project description:Barrett's esophagus transcriptome was analysed and compared with Barrett's esophagus primary cell culture and esophageal adenocarcinoma. Keywords: SAGE analysis to compare tissues Barrett's esophagus biopsy was taken from 1 male metaplastic Barrett's esophagus patient. Barrett's esophagus primary cell culture was cultures from a biopsy taken from a Barrett's esophagus patient and cultured for about 4 to 5 weeks. Esophageal adenocarcinoma was taken from a patient known to have cancer and previously Barrett's esophagus
2006-06-28 | E-GEOD-5155 | biostudies-arrayexpress
Project description:Barrett's esophagus transcriptome was analysed and compared with Barrett's esophagus primary cell culture and esophageal adenocarcinoma. Keywords: SAGE analysis to compare tissues
2006-06-28 | GSE5155 | GEO
Project description:SAGE performed on biopsies of Barrett's esophagus, squamous esophagus and gastric cardia taken from a metaplastic Barrett's esophagus patient. Keywords: SAGE comparative analysis of gene expression profiles of Barrett's esophagus, normal squamous esophagus and gastric cardia tissue
2005-06-20 | E-GEOD-2769 | biostudies-arrayexpress
Project description:SAGE performed on biopsies of Barrett's esophagus, squamous esophagus and gastric cardia taken from a metaplastic Barrett's esophagus patient. Keywords: SAGE
2005-06-20 | GSE2769 | GEO
Project description:Great Ape Copy Number Variation
| PRJNA144461 | ENA
Project description:Barrett's esophagus is a metaplastic condition of the distal esophagus, characterized by the replacement of normal squamous epithelium by columnar epithelium. Patients with BE have an increased risk of developing esophageal adenocarcinoma. MicroRNAs have been implicated to be disease and tissue specific, however limited data of microRNA expression in the esophagus is available. Therefore we evaluated microRNA expression profiles of esophageal adenocarcinoma and compared these with Barrett's esophagus and normal squamous esophagus.
2012-03-15 | GSE29965 | GEO
Project description: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. METHODS: Gene expression profiles for endoscopically obtained biopsy specimens of Barrett's esophagus or esophageal adenocarcinoma and associated normal esophagus and duodenum were identified for 17 patients using DNA microarrays. Unsupervised and supervised approaches for data analysis defined similarities and differences between the tissues as well as correlations with clinical phenotypes. RESULTS: Each tissue displays a unique expression profile that distinguishes it from others. Barrett's esophagus and esophageal adenocarcinoma express a unique set of stromal genes that is distinct from normal tissues but similar to other cancers. Adenocarcinoma also showed lower and higher expression for many genes compared with Barrett's esophagus. No difference in gene expression was found between short-segment and long-segment Barrett's esophagus. CONCLUSIONS: The genome-wide assessment provided by current DNA microarrays reveals many candidate genes and patterns not previously identified. Stromal gene expression in Barrett's esophagus and adenocarcinoma is similar, indicating that these changes precede malignant transformation. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design
2006-10-18 | GSE6059 | GEO