|
| Status |
Public on Jan 01, 2009 |
| Title |
Merkel cell carcinoma tumor 11 |
| Sample type |
genomic |
| |
|
| Source name |
primary merkel cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
Site of Primary: upper limb
Size of Primary Tumor (cm): 1.7
Survival: unknown
AGE: 85
SEX: F
Other: Collision tumor with squamous cell carcinoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
15 micrograms of genomic DNA were digested with AluI and RsaI (New England Biolabs, Ipswich, MA) and purified using the QIAquick PCR Purification Kit (Qiagen). DNA was eluted in water and diluted to 100 nanograms/microliter.
|
| Label |
Cy3
|
| Label protocol |
DNA with was random-prime labeled using the Klenow DNA polymerase, random primers, and cyanine-labeled nucleotides. Test DNA with was labeled with cyanine-3 (Cy3) and the reference DNA was labeled with cyanine-5 (Cy5).
|
| |
|
| Hybridization protocol |
150 microliters of labeled target were added to 50 microliters Cot-1 DNA, 50 microliters blocking agent. 250 microliters of 2X Hybridization Buffer was then added followed by a quick spin. The hybridization mix was denatured by placing in 98 °C heat block for 3 min. Then samples were transfered to 37 °C heat block and incubated for 30 min, followed by centrifugation for 1 min at ~18,000 g. The hybridization chambers and gasket were assembled and the entire 500 microliters were transferred for hybridization to a slide-size array. The slide was then placed at 65 °C in a rotating hybridization oven for 40 h at 20 rpm.
|
| Scan protocol |
The arrays were scanned using the Agilent scanner and feature extraction software.
|
| Description |
none
|
| Data processing |
The raw data were log-transformed and mode-centered.
|
| |
|
| Submission date |
Oct 16, 2008 |
| Last update date |
Oct 23, 2008 |
| Contact name |
Bianca Durando Lemos |
| E-mail(s) |
bcdl@u.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Medicine/Dermatology
|
| Street address |
815 Mercer St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL2879 |
| Series (1) |
| GSE13239 |
Array Comparative Genomic Hybridization of Merkel Cell Carcinoma Tumors |
|
