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Sample GSM3028082 Query DataSets for GSM3028082
Status Public on Mar 02, 2018
Title SCEC and corresponding normal tissue, replicate 1
Sample type genomic
 
Channel 1
Source name SCEC, patient 1
Organism Homo sapiens
Characteristics tissue: middle thoracic SCEC with stage III
Treatment protocol Tissue sections were cut from frozen blocks and then stained with toluidine blue for genomic DNA (gDNA). Carcinoma cells or non-malignant cells were collected from cancerous or adjacent noncancerous tissue sections using LMD (Leica Microsystems, Wetzlar, Germany) by pathologists
Growth protocol A total of 3 SCEC tissues and matched adjacent noncancerous tissues were dissected from the surgical specimens and snap-frozen in liquid nitrogen, then stored at -80°C in the tissue bank of Fudan University Shanghai Cancer Center.
Extracted molecule genomic DNA
Extraction protocol Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), Use Nano Drop (Cat#ND-1000, ThermoFisher, Waltham, MA, US) and 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.
Label Cy5
Label protocol Experimental sample and control sample were labeled with Cy5 NHS ester and Cy3 NHS ester respectively, using Agilent Genomic DNA Labeling Kit PLUS followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane, 30 kDa. Measured the absorbance at A260nm (DNA), A550nm(Cyanine 3), and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.
 
Channel 2
Source name corresponding normal tissue, patient 1
Organism Homo sapiens
Characteristics tissue: control
Treatment protocol Tissue sections were cut from frozen blocks and then stained with toluidine blue for genomic DNA (gDNA). Carcinoma cells or non-malignant cells were collected from cancerous or adjacent noncancerous tissue sections using LMD (Leica Microsystems, Wetzlar, Germany) by pathologists
Growth protocol A total of 3 SCEC tissues and matched adjacent noncancerous tissues were dissected from the surgical specimens and snap-frozen in liquid nitrogen, then stored at -80°C in the tissue bank of Fudan University Shanghai Cancer Center.
Extracted molecule genomic DNA
Extraction protocol Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), Use Nano Drop (Cat#ND-1000, ThermoFisher, Waltham, MA, US) and 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.
Label Cy3
Label protocol Experimental sample and control sample were labeled with Cy5 NHS ester and Cy3 NHS ester respectively, using Agilent Genomic DNA Labeling Kit PLUS followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane, 30 kDa. Measured the absorbance at A260nm (DNA), A550nm(Cyanine 3), and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.
 
 
Hybridization protocol Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit in Hybridization Oven at 65℃, 20rpm for 24 hours.Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set in staining dishes follow the manufacturer's instructions.
Scan protocol Images were quantified using Agilent Feature Extraction Software (version 10.7).
Description Biological replicate from SCEC patient 1
252206030966_1_1
Data processing Agilent data analysis using the agilent cytogenomics software which provides no normalized data on probe level. Therefore, the preliminary results from cytogenomics software are reported in matrix linked at the foot of the Series record.
 
Submission date Mar 01, 2018
Last update date Mar 02, 2018
Contact name Juan Wang
E-mail(s) wangj@rainbow-genome.com
Organization name Shanghai Jiayin Biotechnology Co., Ltd.
Street address No. 135 Guowei Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL10123
Series (2)
GSE111298 aCGH data from SCEC and corresponding normal samples
GSE111299 Genome-wide analysis of gene expression and DNA copy number variations in small cell esophageal carcinoma

Supplementary file Size Download File type/resource
GSM3028082_252206030966_S01_CGH_107_Sep09_1_1.txt.gz 18.7 Mb (ftp)(http) TXT
Processed data are available on Series record

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