|
| Status |
Public on Apr 09, 2019 |
| Title |
FVB_K14Cre-p53f/f-Brca1f/f_121382_primary_CGH_GMurrow |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
FVB Qiagen DNA Reference
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
sample type: Reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen #69504), labeled with a Sure Tag DNA kit (Agilent #5190-4240), and hybridized to 244K CGH microarrays (Agilent #G4415A) as previously described.
|
| Label |
Cy3
|
| Label protocol |
described in Herschkowitz et al., 2012, PNAS, 109:2778-2783
|
| |
|
| Channel 2 |
| Source name |
Mammary Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary Tumor
genotype: K14-Cre; P53 F/F BRCA1 F/F
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen #69504), labeled with a Sure Tag DNA kit (Agilent #5190-4240), and hybridized to 244K CGH microarrays (Agilent #G4415A) as previously described.
|
| Label |
Cy5
|
| Label protocol |
described in Herschkowitz et al., 2012, PNAS, 109:2778-2783
|
| |
|
| |
| Hybridization protocol |
described in Herschkowitz et al., 2012, PNAS, 109:2778-2783
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software
|
| Data processing |
Gene expression was calculated as log2 Cy5/Cy3 ratios, keeping only probes with Lowess normalized intensity values greater than 10 in both Cy5 and Cy3 channels.
|
| |
|
| Submission date |
Nov 01, 2018 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL15076 |
| Series (2) |
| GSE122073 |
A mouse model featuring tissue specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer [aCGH] |
| GSE122076 |
A mouse model featuring tissue specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer |
|
