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Status |
Public on Sep 09, 2010 |
Title |
tumor_ID, 39; patient_ID, 14 |
Sample type |
genomic |
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Channel 1 |
Source name |
human genomic DNA (hepatocellular carcinoma tumor tissue)
|
Organism |
Homo sapiens |
Characteristics |
tumor: HBs-Ag, negative; HCV-ab, positive
|
Treatment protocol |
Frozen at minus 70 degrees until DNA extraction
|
Growth protocol |
Human samples obtained with surgecal resection Human samples obtained with surgecal resection
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted with QIAamp DNA Micro kit (Qiagen, Valencia, CA).
|
Label |
Cy5
|
Label protocol |
The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.
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Channel 2 |
Source name |
Human Genomic DNA, MALE (Promega:G1471)
|
Organism |
Homo sapiens |
Characteristics |
reference: Human Genomic DNA, MALE (Promega:G1471)
|
Treatment protocol |
Frozen at minus 70 degrees until DNA extraction
|
Growth protocol |
Human samples obtained with surgecal resection Human samples obtained with surgecal resection
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted with QIAamp DNA Micro kit (Qiagen, Valencia, CA).
|
Label |
Cy3
|
Label protocol |
The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.
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|
|
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Hybridization protocol |
The samples were hybridized for 24 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.
|
Scan protocol |
Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.
|
Description |
comparison of multiple tumors from same patient
|
Data processing |
Data were extracted using Agilent's Feature Extraction software, version 9.5.3.1 , Cy3 corresponding to the gProcessed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Centralizated Log2Ratio (Cy5/Cy3) was used for the normalization algorithm. Normalized log10 ratio (Cy5/Cy3) was calculated using CGH-v4_95_Feb07 protocol of FE software.
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|
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Submission date |
Jun 30, 2010 |
Last update date |
Sep 09, 2010 |
Contact name |
Kikuya Kato |
Organization name |
Osaka Medical Center for Cancer and Cardiovascular Dieseases
|
Street address |
1-3-3 Nakamichi, Higashinari-ku
|
City |
Osaka |
ZIP/Postal code |
537-8511 |
Country |
Japan |
|
|
Platform ID |
GPL5477 |
Series (1) |
GSE22635 |
Genetic and epigenetic characteristics of human multiple hepatocellular carcinoma |
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