|
| Status |
Public on Jan 05, 2010 |
| Title |
UMUC cell line relative to normal diploid cell |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Normal human diploid genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: normal human genomic DNA purchased from Promega
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromosomal DNA was isolated from BC cell lines using FlexiGene(QIAGEN) according manufacturer's protocol.
|
| 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.
|
| |
|
| Channel 2 |
| Source name |
UMUC genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human bladder cancer UMUC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromosomal DNA was isolated from BC cell lines using FlexiGene(QIAGEN) according manufacturer's protocol.
|
| 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.
|
| |
|
| |
| Hybridization protocol |
The samples were hybridized for 40 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 |
UMUC cell line relative to normal diploid cell
|
| Data processing |
Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the gProcessed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Normalized log10 ratio (Cy5/Cy3) was calculated using CGH-v4_95_Feb07 protocol of FE software.
|
| |
|
| Submission date |
Dec 31, 2009 |
| Last update date |
Jan 04, 2010 |
| Contact name |
Naohiko Seki |
| E-mail(s) |
naoseki@faculty.chiba-u.jp
|
| Phone |
+81-43-226-2971
|
| Organization name |
Chiba University
|
| Department |
Functional Genomics
|
| Street address |
1-8-1, Inohana
|
| City |
Chiba |
| State/province |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE19714 |
Chromosomal aberrations of human bladder cancer cell lines |
|
