|
| Status |
Public on Aug 15, 2007 |
| Title |
PMBCL16 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
PMBCL16
|
| Organism |
Homo sapiens |
| Characteristics |
PMBCL tumor DNA
|
| Extracted molecule |
genomic DNA |
| Label |
Cyanine 3
|
| Label protocol |
Random prime reaction
|
| |
|
| Channel 2 |
| Source name |
Male pooled genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Male pooled genomic reference DNA
|
| Biomaterial provider |
Novagen
|
| Extracted molecule |
genomic DNA |
| Label |
Cyanine 5
|
| Label protocol |
Random prime reaction
|
| |
|
| |
| Hybridization protocol |
Hybridization solution: 80% DIG-easy, 10% sheared herring sperm DNA, 10% yeast tRNA. Probe was blocked using 100ug human CoT-1 DNA and hybridized to the slide at 45C for ~36 hours under a 24x60mm coverslip in a hybrization cassette. Wash: 4X 0.1% SDS/0.1X SSC at 45C. Rinse: 4X 0.1X SSC, room temp. Dried with an oil-free air stream.
|
| Scan protocol |
Scanned at 10um resolution on a Applied Precision Instruments AutoE CCD-based scanner.
|
| Description |
tumor DNA (cy3) hybridized against normal male pooled reference DNA (cy5)
|
| Data processing |
Data was obtained from the scanned image files generated using SoftWoRx Tracker software from Applied Precision. Obtained data was normalized using a three-step normalization procedure; (Khojasteh et al BMC Bioinformatics 2005;6:274).
|
| |
|
| Submission date |
Jan 18, 2007 |
| Last update date |
Aug 15, 2007 |
| Contact name |
Lindsey Kimm |
| E-mail(s) |
[email protected]
|
| Organization name |
BC Cancer Research Centre
|
| Department |
Cancer Genetics
|
| Lab |
Wan Lam Lab
|
| Street address |
675 W10th Ave
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2735 |
| Series (1) |
| GSE7383 |
Frequent occurrence of deletions in primary mediastinal B-cell lymphoma |
|
| Data table header descriptions |
| ID_REF |
|
| Spot Mean Intensity (Cy3) |
Mean spot pixel intensity - cy3 channel |
| Spot Mean Intensity (Cy5) |
mean spot pixel intensity - cy5 channel |
| Background Median Intensity (Cy3) |
median background pixel intensity - cy3 channel |
| Background Median Intensity (Cy5) |
median background pixel intensity - cy5 channel |
| Spot Normalized Intensity (Cy3) |
spot mean with background subtracted - cy3 channel |
| Spot Normalized Intensity (Cy5) |
spot mean with background subtracted - cy5 channel |
| Spot SNR (Cy3) |
signal to noise ratio - cy3 channel |
| Spot SNR (Cy5) |
signal to noise ratio - cy5 channel |
| Spot Ratio (Cy3) |
Cy3/Cy5 ratio |
| Spot Ratio (Cy5) |
Cy5/Cy3 ratio |
| Spot Log2 Ratio (Cy3) |
Log2 ratio (Cy3/Cy5) - global mean set to 0 |
| VALUE |
normalized log2 ratio (Cy3/Cy5) |
