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Sample GSM453825 Query DataSets for GSM453825
Status Public on Oct 02, 2009
Title 1064-12c
Sample type genomic
 
Channel 1
Source name Pooled female blood DNA
Organism Homo sapiens
Characteristics tissue: normal blood
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by the QIAamp DNA micro kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, and amplified by the GenomiPhi whole genome amplification system (Amersham, Piscataway, NJ).
Label Cy3
Label protocol DNA was labeled with aminoallyl-dUTP (Ambion, Austin, TX) by adding 1.5μl of the reagent directly to the normal GenomiPhi reaction prior to overnight incubation at 30°C. Similar amplification and labeling was performed on a commercially available genomic female control DNA (Promega, San Luis Obispo, CA). Amplified DNA was then digested with HaeIII digestion enzyme (N.E. Biosciences, Ipswich, MA) and quantified by PicoGreen dsDNA quantitation (Molecular Probes, Eugene, OR). A minimum of 8.0μg DNA was then precipitated overnight at -80°C, washed with 70% ethanol, and vacuum dried. Control/tumor pairs were then resuspended in sodium bicarbonate buffer (pH 9.0), and coupled with 3.0μl Cy3/Cy5 dye (Amersham) for 1.5 hours at room temperature. After coupling, the reaction was quenched with 4M hydroxylamine, control/tumor pairs were combined into one tube, and remaining uncoupled dye was removed by passing the samples through NucAway spin columns (Ambion). COT human DNA and yeast tRNA (Roche, Indianapolis, IN) were then added to the column flow-through and dried by vacuum centrifugation.
 
Channel 2
Source name DNA from microdissected tumor tissue 1064
Organism Homo sapiens
Characteristics tissue: high-grade late stage serous tumor
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by the QIAamp DNA micro kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, and amplified by the GenomiPhi whole genome amplification system (Amersham, Piscataway, NJ).
Label Cy5
Label protocol DNA was labeled with aminoallyl-dUTP (Ambion, Austin, TX) by adding 1.5μl of the reagent directly to the normal GenomiPhi reaction prior to overnight incubation at 30°C. Similar amplification and labeling was performed on a commercially available genomic female control DNA (Promega, San Luis Obispo, CA). Amplified DNA was then digested with HaeIII digestion enzyme (N.E. Biosciences, Ipswich, MA) and quantified by PicoGreen dsDNA quantitation (Molecular Probes, Eugene, OR). A minimum of 8.0μg DNA was then precipitated overnight at -80°C, washed with 70% ethanol, and vacuum dried. Control/tumor pairs were then resuspended in sodium bicarbonate buffer (pH 9.0), and coupled with 3.0μl Cy3/Cy5 dye (Amersham) for 1.5 hours at room temperature. After coupling, the reaction was quenched with 4M hydroxylamine, control/tumor pairs were combined into one tube, and remaining uncoupled dye was removed by passing the samples through NucAway spin columns (Ambion). COT human DNA and yeast tRNA (Roche, Indianapolis, IN) were then added to the column flow-through and dried by vacuum centrifugation.
 
 
Hybridization protocol Dried DNA pallet was reconstituted in SlideHyb buffer I (Ambion) and hybridized onto a 22K 60mer oligonucleotide array platform (provided by the microarray core facility at the Advanced Technology Center, National Cancer Institute) overnight at 42°C using a GeneMachines Hyb4 slide hybridization machine (Genomic Solutions, Ann Arbor, MI).
Scan protocol Scanning was performed on a ScanArray 4000XL Microarray Analysis System, and quantified using ScanArray Express (Perkin Elmer, Downers Grove, IL).
Description Microdissected ovrian cancer tissue sample
Data processing LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. ScanArray Express software (Perkin Elmer) was used.
 
Submission date Sep 17, 2009
Last update date Oct 01, 2009
Contact name Samuel Mok
E-mail(s) scmok@mdanderson.org
Organization name University of Texas M.D. Anderson Cancer Center
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL9216
Series (1)
GSE18154 Genetic changes in high-grades serous ovarian cancer

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference
RATIO normalized ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE RATIO
1 0.2388 1.18
2 0.7312 1.66
3 -1.5146 0.35
4 -0.3219 0.8
5 -1.2863 0.41
6 -1.1203 0.46
7 0.3674 1.29
8 -0.0439 0.97
9 0.0286 1.02
10 0.7570 1.69
11 0.5945 1.51
12 0.4330 1.35
13 -0.4739 0.72
14 -0.0145 0.99
15 0.5160 1.43
16 1.7398 3.34
17 0.8718 1.83
18 0.8718 1.83
19 1.1763 2.26
20 -0.0439 0.97

Total number of rows: 22464

Table truncated, full table size 389 Kbytes.




Supplementary file Size Download File type/resource
GSM453825.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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