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Sample GSM1010596 Query DataSets for GSM1010596
Status Public on Jan 22, 2015
Title CC with lung metastasis PEM-11P primary
Sample type genomic
 
Channel 1
Source name CC with lung metastasis
Organism Homo sapiens
Characteristics tissue: cholangiocarcinoma
gender: M
pair: PEM-11
Extracted molecule genomic DNA
Extraction protocol Phenol/Chloroform Extraction Protocol: Genomic tumor cell DNA was isolated from microdissected fresh frozen clinical tumor samples using proteinaseK digestion (P2308, Sigma-Aldrich, St. Louis, MO) and subsequent Phenol/Chlororform extraction.
Label Cy5
Label protocol Cy5: Five micrograms of genomic DNA were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; Valencia, CA) and labeled and 60 µM Cy5-dUTP (GE Amersham, Piscataway, NJ). Tumor DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).
Cy3: Five micrograms of reference DNA of the opposite gender (human genomic DNA, Promega, San Luis Obispo, CA) were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, Valencia, CA) and labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy3-dUTP (GE Amersham, Piscataway, NJ). Reference DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).
 
Channel 2
Source name Female human genomic DNA, Promega, G152A
Organism Homo sapiens
Characteristics gender: F
sample type: Female human genomic DNA, Promega, G152A
Extracted molecule genomic DNA
Extraction protocol Phenol/Chloroform Extraction Protocol: Genomic tumor cell DNA was isolated from microdissected fresh frozen clinical tumor samples using proteinaseK digestion (P2308, Sigma-Aldrich, St. Louis, MO) and subsequent Phenol/Chlororform extraction.
Label Cy3
Label protocol Cy5: Five micrograms of genomic DNA were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; Valencia, CA) and labeled and 60 µM Cy5-dUTP (GE Amersham, Piscataway, NJ). Tumor DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).
Cy3: Five micrograms of reference DNA of the opposite gender (human genomic DNA, Promega, San Luis Obispo, CA) were digested with the restriction enzymes AluI and RsaI (10U/uL; Invitrogen, Carlsbad, CA). Digested DNA was purified using QIAprep Spin Miniprep Kit (QIAGEN, Valencia, CA) and labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy3-dUTP (GE Amersham, Piscataway, NJ). Reference DNA was pooled, purified and concentrated to 79 µl using Vivaspin 500 concentrator (VS0122, 30k MWCO, Vivascience, Littleton, MA).
 
 
Hybridization protocol According to Agilent user guide.
Scan protocol Dried array slides were scanned using the DNA Microarray Scanner (Agilent, Santa Clara, CA).
Data processing Raw image files of the arrays were processed using Feature Extraction software 8.1 using default CGH parameters (Agilent, Santa Clara, CA). Spot values were normalized using the default linear-lowess normalization.
 
Submission date Sep 27, 2012
Last update date Jan 22, 2015
Contact name Xin Wei Wang
E-mail(s) xw3u@nih.gov
Phone 240-760-6858
Organization name National Cancer Institute
Department Laboratory of Human Carcinogenesis
Lab Liver Carcinogenesis Unit
Street address 37 Convent Drive
City Bethesda
State/province MD
ZIP/Postal code 20892-4255
Country USA
 
Platform ID GPL9075
Series (1)
GSE41210 Integrative genomic and transcriptomic characterization of matched primary and metastatic liver and colorectal carcinoma

Data table header descriptions
ID_REF
VALUE default linear-lowess normalization log10 Cy5/Cy3

Data table
ID_REF VALUE
A_14_P112718 0.383882392
A_16_P15000916 0.383882392
A_16_P15001074 0.383882392
A_16_P00000012 -0.490540891
A_16_P00000021 -0.490540891
A_16_P00000023 -0.490540891
A_16_P00000027 -0.490540891
A_16_P00000036 -0.490540891
A_16_P15001533 -0.490540891
A_16_P15001594 -0.490540891
A_16_P00000099 -0.490540891
A_16_P00000114 -0.490540891
A_16_P00000136 -0.490540891
A_16_P15001775 -0.490540891
A_16_P00000179 -0.490540891
A_16_P00000195 -0.490540891
A_16_P15001886 -0.490540891
A_16_P00000237 -0.490540891
A_16_P00000289 -0.490540891
A_14_P114030 -0.490540891

Total number of rows: 98735

Table truncated, full table size 2549 Kbytes.




Supplementary file Size Download File type/resource
GSM1010596_PEM-11A_251469811421_S01_CGH_105_1_1.txt.gz 10.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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