|
| Status |
Public on Aug 02, 2011 |
| Title |
Normal mammary tissue |
| Sample type |
genomic |
| |
|
| Source name |
normal mammary tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mammary tissue
disease state: normal
|
| Treatment protocol |
None.
|
| Growth protocol |
Tumor biopsies.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs were extracted from frozen tumor biopsies using Qiagen's All Prep DNA kit. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated, fragmented PCR products were prepared according to the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3) starting with 500 ug of mouse genomic DNA.
|
| |
|
| Hybridization protocol |
At least 225 ug of biotinylated, fragmented PCR products were hybridized for 16 hr at 50C on Affymetrix Mouse Diversity Genotyping Arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
The arrays were scanned using an Affymetrix GeneChip Scanner 3000.
|
| Description |
Control
|
| Data processing |
CEL files were generated using the GeneChip software (Affymetrix). Data was analyzed using the SNP array data processing modules of the software suite, dChip (http://www.biostat.harvard.edu/complab/dchip/snp.htm). Data processing on model-based expression was performed using the PM/MM model. Permutation using Hidden Markov Model (HMM) score and normalization was performed using the reference normalization algorithm developed at St. Jude (Nature 2007;446:758-764 [PMID 17344859]).
|
| |
|
| Submission date |
Mar 04, 2011 |
| Last update date |
Aug 02, 2011 |
| Contact name |
jean zhao |
| E-mail(s) |
jean_zhao@dfci.harvard.edu
|
| Organization name |
dana-farber cancer institute
|
| Department |
cancer biology
|
| Lab |
zhao
|
| Street address |
450 Brookline Ave
|
| City |
boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13147 |
| Series (1) |
| GSE27691 |
Affymetrix SNP array data for mammary tumors that recurred after inactivation of the oncogenic PIK3CA-H1047R |
|
