|
| Status |
Public on Sep 12, 2007 |
| Title |
breast tumor - I419 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Cryobanked tumor Pat_ID I419
|
| Organism |
Homo sapiens |
| Characteristics |
ER Status: ER+
PR Status: PR+
ErBB2 amplification: NO
age: 71
grade: 2
stage: 4
node: 2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified from frozen tumor powders using High Pure PCR Preparation Kit (Roche Diagnostics; Indianapolis, Indiana
|
| Label |
Cy3
|
| Label protocol |
400-600 ng of reference and test genomic DNA was labeled with Cy5 and Cy3 respectively (using the BioPrime kit from Invitrogen). The DNA was denatured in the presence of random primer at 100 ║C for 10 minutes. Labeling occurred with the addition of Cy5 to the reference DNA and Cy3 to the test DNA and Klenow. Incubation took place overnight at 37║C in a thermalcycler. The unincorporated nucleotides were removed using a MicroSpin G-25 Columns (Amersham).
|
| |
|
| Channel 2 |
| Source name |
Normal Blood
|
| Organism |
Homo sapiens |
| Characteristics |
Normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified from frozen tumor powders using High Pure PCR Preparation Kit (Roche Diagnostics; Indianapolis, Indiana
|
| Label |
Cy5
|
| Label protocol |
400-600 ng of reference and test genomic DNA was labeled with Cy5 and Cy3 respectively (using the BioPrime kit from Invitrogen). The DNA was denatured in the presence of random primer at 100 ║C for 10 minutes. Labeling occurred with the addition of Cy5 to the reference DNA and Cy3 to the test DNA and Klenow. Incubation took place overnight at 37║C in a thermalcycler. The unincorporated nucleotides were removed using a MicroSpin G-25 Columns (Amersham).
|
| |
|
| |
| Hybridization protocol |
The test and reference probes were combined with 35 ╡g of Cot-1 DNA in 1.5mL tube and ethanol precipitated. Following centrifugation (30 min at 14000 rpm), the probes were re-suspended in 5 ╡l of water, 10 ╡l 20% SDS and 35 ╡l of Master Mix #1, heated to 73║C for 10 minutes and incubated for 60 minutes at 37║C to block repetitive elements on the probe. Hybridization was performed for 48 hours at 37║C. After hybridization, the slides were washed with PN solution at room temperature followed by a 15 min wash with wash solution (50% Formamide, 2X SSC, pH 7). DAPI was applied to the slides for Image analysis using a custom built CCD camera system
|
| Scan protocol |
Image analysis using a custom built CCD camera system
|
| Description |
aCGH data from ER+ breast tumor
|
| Data processing |
Data analysis was carried out using UCSF Spot software. SPROC software was used to automatically filter the data to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 and low reference/DAPI signal intensity. Observations with standard deviation of replicates grater then 0.2 were declared missing.
|
| |
|
| Submission date |
Aug 16, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Christina Yau |
| E-mail(s) |
[email protected]
|
| Phone |
415-209-2248
|
| Organization name |
Buck Institute of Age Research
|
| Lab |
Benz Lab
|
| Street address |
8001 Redwood Blvd
|
| City |
Novato |
| State/province |
CA |
| ZIP/Postal code |
94945 |
| Country |
USA |
| |
|
| Platform ID |
GPL4999 |
| Series (1) |
| GSE8801 |
aCGH data from age-dichotomized ER+ breast tumors |
|
