|
| Status |
Public on Dec 06, 2006 |
| Title |
F5 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
NA10842
|
| Organism |
Homo sapiens |
| Characteristics |
B-lymphocyte cell line DNA, father of pedigree XC01423
|
| Biomaterial provider |
Coriell Cell Repositories
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?NA10842
Coriell
|
| Extracted molecule |
genomic DNA |
| Label |
Cyanine 3
|
| |
|
| Channel 2 |
| Source name |
Mref
|
| Organism |
Homo sapiens |
| Characteristics |
single male reference genomic DNA
|
| Biomaterial provider |
anonymous normal male donor
Coriell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp DNA Blood Maxi Kit (QIAGEN Inc.)
|
| Label |
Cyanine 5
|
| |
|
| |
| Description |
cyanine 3 = sample
cyanine 5 = reference
|
| Data processing |
three-step normalization procedure; (Khojasteh et al BMC Bioinformatics 2005;6:274)
|
| |
|
| Submission date |
Jul 28, 2006 |
| Last update date |
Dec 06, 2006 |
| Contact name |
Kendy Wong |
| E-mail(s) |
kwong@bccrc.ca
|
| Phone |
604-675-8000
|
| Organization name |
BC Cancer Research Center
|
| Department |
Cancer Genetics
|
| Lab |
Wan Lam Lab
|
| Street address |
675 West 10th Avenue
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2616 |
| Series (1) |
| GSE5442 |
A comprehensive analysis of copy number variations in the human genome |
|
| Data table header descriptions |
| ID_REF |
|
| Spot Mean Intensity (w595) |
Mean Spot Pixel Intensity - Cy3 channel |
| Spot Mean Intensity (w685) |
Mean Spot Pixel Intensity - Cy5 channel |
| Background Median Intensity (w595) |
Median Background Pixel Intensity - Cy3 channel |
| Background Median Intensity (w685) |
Median Background Pixel Intensity - Cy5 channel |
| Spot Normalized Intensity (w595) |
Spot Mean - Background Median |
| Spot Normalized Intensity (w685) |
Spot Mean - Background Median |
| Spot SNR (w595) |
Signal to noise ratio - Cy3 |
| Spot SNR (w685) |
Signal to noise ratio - Cy5 |
| Spot Ratio (w595) |
Cy3/Cy5 |
| Spot Ratio (w685) |
Cy5/Cy3 |
| Spot Log2 Ratio (w595) |
log2(Cy3/Cy5) (global mean set to 0) |
| VALUE |
normalized log2 (Cy3/Cy5; sample/ref) |
