|
| Status |
Public on Nov 18, 2011 |
| Title |
X5824 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Genomic DNA from oral dysplasia
|
| Organism |
Homo sapiens |
| Characteristics |
age: 62
gender: M
site: tongue
histology: severe
prior cancer: Unknown
cancer progression: Unknown
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted from microdissected formalin fixed paraffin embedded tissue sections by digestion with proteinase K followed by a phenol chloroform extraction
|
| Label |
Cy3
|
| Label protocol |
Test and reference samples labeled with Cy3 and Cy5 respectively using a random priming reaction in a 25 μL reaction to label genomic DNA
|
| |
|
| Channel 2 |
| Source name |
Normal human genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted from microdissected formalin fixed paraffin embedded tissue sections by digestion with proteinase K followed by a phenol chloroform extraction
|
| Label |
Cy5
|
| Label protocol |
Test and reference samples labeled with Cy3 and Cy5 respectively using a random priming reaction in a 25 μL reaction to label genomic DNA
|
| |
|
| |
| Hybridization protocol |
Labeled test (600ng) and reference (600ng) DNA was hybridized with human Cot-1 DNA for ~ 48 hours at 37°C to arrays of 2464 BAC clones spotted in triplicate (HumArray3.2, UCSF Helen Diller Family Comprehensive Cancer Center Microarray Core). Slides were washed with 50% formamide, 2X SSC for 15 minutes at 45°C followed by a 15 minute wash in PN buffer (0.1M phosphate buffer in 0.1% Nonidet P40) at room temperature. Slides were mounted in a DAPI solution to stain the array spots (90% glycerol, 10% PBS, 1μM DAPI) and imaged.
|
| Scan protocol |
DAPI, Cy3 and Cy5 images were acquired using a custom CCD camera system
|
| Description |
DNA isolated from banked blood (buffy coat)
|
| Data processing |
Array image quantitation was done with UCSF Spot. After quality filtering on spots and clones, an in-house SpotCorrection algorithm was used to remove systematic geometric and GC content effects. Replicate spot averaging and median centering were then performed. A remaining 'paraffin-embedded effect' was removed as follows. For tumor profiles with paired normals, we applied noise reduction using the normal sample as template. The magnitude of the effect was estimated using the derivative log ratio spread (DLRS) [Agilent]. For the two tumor profiles without a paired normal (and AB029 and AB067), we employed the per-probe median of the normal profiles as a normal template, with DLRS scaling as above. Clones without mapping information were excluded. Also, clones of possibly poor quality where more than 50% of the samples had missing data were excluded. Then replicate clones were averaged.
The paired normals for the tumor samples did not have processed normalized data; therefore, these Samples are tableless. The normal data only played a role in the pre-processing stage that generated the processed tumor data.
|
| |
|
| Submission date |
Apr 05, 2011 |
| Last update date |
Nov 18, 2011 |
| Contact name |
Taku Tokuyasu |
| E-mail(s) |
tokuyasu@cc.ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Helen Diller Family Comprehensive Cancer Center
|
| Street address |
1450 3rd Street, HD555
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158-9001 |
| Country |
USA |
| |
|
| Platform ID |
GPL4999 |
| Series (1) |
| GSE28407 |
Diverse routes to oral cancer differing in genome instability and risk for cervical node metastasis |
|
