|
| Status |
Public on Apr 22, 2010 |
| Title |
Carcinoid 13 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Clinical sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
age: 46
sclc/carcinoid: Carcinoid
sclc primary tumor/metastasis: N/A
bronchial/gi carcinoid: Bronchial carcinoid
origin of sample: Lung/lobectomy
growth pattern of cell line: N/A
pathological review: Typical carcinoid
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was isolated from cell lines, cytology specimens or deparaffinated FFPE specimens using reagents of the DNeasy Blood and Tissue Kit, QIAquick PCR Purification Kit (Qiagen, Gaithersburg, MD) as well as Dako Target Retrieval Solution (Dako, Carpinteria, CA) in protocols optimized for maximum yield from the various types of samples.
|
| Label |
Cy5
|
| Label protocol |
500ng sample and reference genomic DNA were fragemented by incubation at 95'C up to 10 min and then were labeled with Cy5 and Cy3, respectively at 85'C for 30 min. Labeled DNA were purified using Agilent KREApure column. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nmCy5).
|
| |
|
| Channel 2 |
| Source name |
Promega male human genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
reference: Promega male human genomic DNA
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was isolated from cell lines, cytology specimens or deparaffinated FFPE specimens using reagents of the DNeasy Blood and Tissue Kit, QIAquick PCR Purification Kit (Qiagen, Gaithersburg, MD) as well as Dako Target Retrieval Solution (Dako, Carpinteria, CA) in protocols optimized for maximum yield from the various types of samples.
|
| Label |
Cy3
|
| Label protocol |
500ng sample and reference genomic DNA were fragemented by incubation at 95'C up to 10 min and then were labeled with Cy5 and Cy3, respectively at 85'C for 30 min. Labeled DNA were purified using Agilent KREApure column. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nmCy5).
|
| |
|
| |
| Hybridization protocol |
Appropriate equal amoung of Cy5-labeled sample and Cy3-labeled reference DNAwere mixed to a 22ul final volumn. 61ul Hybridization Master Mix (1mg/ml Cot-1 DNA 5ul, Agilent 100X blocking agent 1ul, and Agilent 2X HiRPM Hybridization buffer 55ul) was added and incubated at 95'C for 3 min folloed by 37'C for 30min. 27ul of Agilent-CGHBlock was then added and mixed. The hybridization sample mixture was applied onto the microarray gasket well and was covered by a microarray slide. The slide was incubated in a 65'C rotator rack for 40 hours. After hybridization, slide was washed sequential.
|
| Scan protocol |
Scanned on an Agilent DNA microarray scanner
Images were quantified using Agilent Feature Extraction Software v10.5
|
| Description |
n/a
|
| Data processing |
Agilent Feature Extraction Software v10.5 was used for background subtraction and data processing. Data were normalized using Linear method.
|
| |
|
| Submission date |
Apr 22, 2010 |
| Last update date |
Apr 22, 2010 |
| Contact name |
Jih-Hsiang Lee |
| E-mail(s) |
leej15@mail.nih.gov
|
| Organization name |
National Cancer Institute
|
| Department |
Medical oncology branch
|
| Street address |
9000 Rockville Pike, building 10 8N254
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20852 |
| Country |
USA |
| |
|
| Platform ID |
GPL10123 |
| Series (1) |
| GSE21468 |
Array CGH-based Characterization of Genetic Alterations in Pulmonary Neuroendocrine Tumors |
|
