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Series GSE68662 Query DataSets for GSE68662
Status Public on Jan 13, 2016
Title Copy number variation analysis of human Barrett's esophagus stem cells (HumanOmniZhongHua-8 v1.0 Beadchip)
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary 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.
 
Overall design 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.
 
Contributor(s) Yamamoto Y, Wang X, Nguyen H, Kern F, Hu Y, Duleba M, Zhang T, Xian W, McKeon F
Citation(s) 26783136
Submission date May 07, 2015
Last update date Apr 13, 2016
Contact name Frank McKeon
E-mail(s) mckeon.xian@gmail.com
Phone 8608372486
Organization name University of Houston
Department Biology and Biochemistry
Street address 3455 Cullen Blvd
City Houston
State/province TX
ZIP/Postal code 77004
Country USA
 
Platforms (1)
GPL20166 Illumina HumanOmniZhongHua-8 v1.0 Beadchip
Samples (8)
GSM1678671 Patient 1 blood
GSM1678672 1DE1
GSM1678673 1C1
This SubSeries is part of SuperSeries:
GSE68664 Copy number variation analysis of human Barrett's esophagus stem cells
Relations
BioProject PRJNA283320

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68662_8samples_Zhonghua8V1_0_MatrixProcessed.csv.gz 86.5 Mb (ftp)(http) CSV
GSE68662_8samples_Zhonghua8V1_0_MatrixSignalIntensity.csv.gz 59.8 Mb (ftp)(http) CSV
GSE68662_RAW.tar 190.1 Mb (http)(custom) TAR (of IDAT)
Processed data are available on Series record

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