|
| Status |
Public on Dec 01, 2008 |
| Title |
D562 cell line relative to normal diploid cell |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Normal human diploid genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Purchased from Promega
|
| Growth protocol |
Five of the esophageal squamous cell carcinoma (ESCC) cell lines (TE1, TE2, TE3, YES1, and YES2) were maintained in RPMI1640 (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Hyclone, Logan, UT). Five of the (HNSCC) cell lines (Ca9-22, H1, HSC2, HSC3, and D562) were maintained in DMEM (Dulbecco’s modified Eagle medium) /F12 (Invitrogen) with 10% fetal bovine serum (Hyclone). These cells were cultured in 5% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromosomal DNA was isolated from ESCC and HNSCC 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 |
D562
|
| Organism |
Homo sapiens |
| Characteristics |
Pharyngeal squamous cell carcinoma cell line
|
| Growth protocol |
Five of the esophageal squamous cell carcinoma (ESCC) cell lines (TE1, TE2, TE3, YES1, and YES2) were maintained in RPMI1640 (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Hyclone, Logan, UT). Five of the (HNSCC) cell lines (Ca9-22, H1, HSC2, HSC3, and D562) were maintained in DMEM (Dulbecco’s modified Eagle medium) /F12 (Invitrogen) with 10% fetal bovine serum (Hyclone). These cells were cultured in 5% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromosomal DNA was isolated from ESCC and HNSCC 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 |
D562 cell line relative to normal duploid cell
|
| Data processing |
Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the Processed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Normalized log2 ratio (Cy3/Cy5) was calculated using CGH-v4_95_Feb07 protocol of FE software.
|
| |
|
| Submission date |
Jun 30, 2008 |
| Last update date |
Sep 24, 2008 |
| Contact name |
Katsuyuki Hayashi |
| E-mail(s) |
hayashi@dna-chip.co.jp
|
| Organization name |
DNA Chip Research Inc
|
| Department |
Business Development
|
| Street address |
1-1-43, Suehiro-cho
|
| City |
Tsurumi-ku, Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE11938 |
Chromosomal aberration of ESCC and HSCC cell lines |
|
