|
Status |
Public on Dec 01, 2008 |
Title |
H1 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.
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|
|
Channel 2 |
Source name |
H1
|
Organism |
Homo sapiens |
Characteristics |
Oral 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 |
H1 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.
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|
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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 |
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