|
| Status |
Public on Jul 01, 2009 |
| Title |
Oral109 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Oral_Specimen_109
|
| Organism |
Homo sapiens |
| Characteristics |
Formalin-fixed paraffin-embedded oral specimen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All lesions were microdissected, and the dissected tissues were places in sodium dodecyl sulfate/proteinase K at 55°C and spiked twice a day for 72 hours with fresh proteinase K. Genomic DNA was extracted with phenol/chloroform and with ethanol.
|
| Label |
Cy3
|
| Label protocol |
Random prime probe labeling was performed to label sample and reference genomic DNA (250ng each). Each reaction was labeled with either 2 nmol of cyanine-3 or cyanine-5 dCTP.
|
| |
|
| Channel 2 |
| Source name |
Normal male
|
| Organism |
Homo sapiens |
| Characteristics |
Novagen pooled normal male genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purchased genomic DNA.
|
| Label |
Cy5
|
| Label protocol |
Random prime probe labeling was performed to label sample and reference genomic DNA (250ng each). Each reaction was labeled with either 2 nmol of cyanine-3 or cyanine-5 dCTP.
|
| |
|
| |
| Hybridization protocol |
Probes were combined, denatured and annealed in a solution containing 100 ug human Cot-1 DNA (Invitrogen) and 48 ul DIG Easy hybridization solution (Roche) containing sheared herring sperm DNA (Sigma-Aldrich) and yeast tRNA (Calbiochem). Probe was denautred at 85°C for 5 minutes, and repetitive sequences were blocked at 45°C for 1 hour prior to hybridization. The probe mixture was applied to the slide surface and hybridized for 36 hrs at 45°C. The arrays were washed 5 times in 0.1X SSC, 0.1% SDS at room temperature with agitation. Each array was then rinsed repeatedly in 0.1X SSC and dried by centrifugation.
|
| Scan protocol |
A charge-coupled device (CCD) scanner system (ARrayworx eAuto, API, Issaquah, WA) was used to determine the signal intensities of the Cyanine 5/Cyanine3 channels. Arrays were scanned at a 9.75um resolution; exposure times for each image wavelength were usually between 0.2 to 2 sec. Images were analyzed by SoftWoRx Tracker analysis software (Applied Precision, Issaquah, WA, USA).
|
| Description |
N/A
|
| Data processing |
A three-step normalization procedure [Khojasteh et al. BMC Bioinformatics 6:274, 2005] was performed to each raw data.
|
| |
|
| Submission date |
Apr 26, 2008 |
| Last update date |
Feb 20, 2009 |
| Contact name |
T Buys |
| Organization name |
British Columbia Cancer Research Centre
|
| Department |
Cancer Genetics and Developmental Biology
|
| Lab |
Wan Lam Lab
|
| Street address |
675 W.10th Avenue
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2616 |
| Series (1) |
| GSE11275 |
Tiling-set aCGH data for oral dysplasias and oral squamous cell carcinomas |
|
| Data table header descriptions |
| ID_REF |
|
| Spot Mean Intensity (w595) |
Mean intensity of spot for Cy3 channel |
| Spot Mean Intensity (w685) |
Mean intensity of spot for Cy5 channel |
| Background Median Intensity (w595) |
Median signal intensity from area around spot for Cy3 channel |
| Background Median Intensity (w685) |
Median signal intensity from area around spot for Cy5 channel |
| Spot Normalized Intensity (w595) |
Locally normalized value for mean intensity of spot for Cy3 channel |
| Spot Normalized Intensity (w685) |
Locally normalized value for mean intensity of spot for Cy5 channel |
| Spot SNR (w595) |
Column "Spot Mean Intensity (w595)" divided by column "Background Median Intensity (w595)" |
| Spot SNR (w685) |
Column "Spot Mean Intensity (w685)" divided by column "Background Median Intensity (w685)" |
| Spot Ratio (w595) |
Column "Spot Normalized Intensity (w595)" divided by column "Spot Normalized Intensity (w685)" |
| Spot Ratio (w685) |
Column "Spot Normalized Intensity (w685)" divided by column "Spot Normalized Intensity (w595)" |
| Spot Log2 Ratio (w595) |
log2 for column labeled "Spot Ratio (595)" |
| VALUE |
log 2 ratio test/reference (Spot log2 ratio (w595) column following spatial bias normalization) |
