|
| Status |
Public on Sep 09, 2010 |
| Title |
tumor_ID, 6; patient_ID, 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
human genomic DNA (hepatocellular carcinoma tumor tissue)
|
| Organism |
Homo sapiens |
| Characteristics |
tumor: HBs-Ag, positive; HCV-ab, negative
|
| 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.
|
| |
|
| 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.
|
| |
|
| |
| 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.
|
| |
|
| 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 |
|
