|
| Status |
Public on Nov 22, 2011 |
| Title |
CGH_TO_2900c_1056o_10L |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Lung tumor from KrasLA2 mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
tissue: Lung tumor
tumor_group: 1
|
| Growth protocol |
Mice were fed standard chow and allowed water ad libitum. Mice were sacrificed at 6 months of age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Dneasy Tissue kit (Qiagen) and further purified by phenol/choroform extraction.
|
| Label |
Cy3
|
| Label protocol |
We labeled 1 μg of test (tumor) DNA and reference genomic DNA (normal lung) with CY3 and CY5 (Amersham), respectively.
|
| |
|
| Channel 2 |
| Source name |
Normal lung from KrasLA2 mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
tissue: Normal lung
|
| Growth protocol |
Mice were fed standard chow and allowed water ad libitum. Mice were sacrificed at 6 months of age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Dneasy Tissue kit (Qiagen) and further purified by phenol/choroform extraction.
|
| Label |
Cy5
|
| Label protocol |
We labeled 1 μg of test (tumor) DNA and reference genomic DNA (normal lung) with CY3 and CY5 (Amersham), respectively.
|
| |
|
| |
| Hybridization protocol |
The test and reference DNAs were hybridized to the BAC arrays for ~48 hrs at 37C. After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 uM DAPI and sealed with a cover slip.
|
| Scan protocol |
A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998). Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).
|
| Data processing |
Images were segmented and quantified using custom software. Data were normalized to the median log2 ratio of Cy3/Cy5. All clones except those mapping to chromosome six, known to be frequently altered in KrasLA2 lung tumors, were used for normalization. The mean and standard deviation (s.d.) of the normalized log2 ratios of the quadruplicate spots were calculated. Clones were declared missing if their ratio was based only on a single spot or their s.d. exceeded 0.2.
|
| |
|
| Submission date |
May 11, 2011 |
| Last update date |
Nov 22, 2011 |
| Contact name |
David Quigley |
| Organization name |
UCSF
|
| Department |
Helen Diller Comprehensive Cancer Center
|
| Lab |
Ashworth Lab
|
| Street address |
1450 Third St. Room 207
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL13520 |
| Series (1) |
| GSE29230 |
Progressive genomic instability in the FVB/KrasLA2 mouse model of lung cancer |
|
