|
| Status |
Public on Dec 17, 2013 |
| Title |
Murine HGSC, T5433 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: BRCA2-/-P53-/-PTEN-/-
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse genomic DNA was isolated using Gentra Puregene Cell Kit (Qiagen) according to the manufacturer’s instructions
|
| Label |
Cy5
|
| Label protocol |
Briefly, reference and test DNA were first fragmented using a heat block at 95°C for 5 minutes and then labeled using Cyanine3 / Cyanine5 fluorescence labeled nucleotides respectively, according to the BioPrime Array CGH Genomic Labeling protocol (Invitrogen).Labeled DNA was purified using Amicon® Ultra-0.5 30k purification columns (Millipore).
|
| |
|
| Channel 2 |
| Source name |
Normal mouse fallopian tubes
|
| Organism |
Mus musculus |
| Characteristics |
reference sample: Pooled DNA from normal fallopian tube of three mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse genomic DNA was isolated using Gentra Puregene Cell Kit (Qiagen) according to the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Briefly, reference and test DNA were first fragmented using a heat block at 95°C for 5 minutes and then labeled using Cyanine3 / Cyanine5 fluorescence labeled nucleotides respectively, according to the BioPrime Array CGH Genomic Labeling protocol (Invitrogen).Labeled DNA was purified using Amicon® Ultra-0.5 30k purification columns (Millipore).
|
| |
|
| |
| Hybridization protocol |
Test and reference DNA were combined and hybridized to the Agilent 1M mouse catalog array for 40 hours at 65°C. The array slides were then washed and scanned.
|
| Scan protocol |
Arrays were scanned using the Agilent G2565AA scanner
|
| Description |
Raw data file - " T5433_Tube_US85003610_252741410697_S01_CGH_105_Jan09", linked to the processed FASST2 segmentation data file - "T5433_Tube_US85003610_252741410697_regions121012", from Nexus Software
|
| Data processing |
Probes signal intensities were obtained using the feature extraction software from Agilent for further analysis. In Feature Extraction software, for CGH data, linear normalization method is used. Analysis was performed with Nexus software (BioDiscovery), for identification of copy number alterations. FASST2 segmentation algorithm was applied by setting the following parameters. A minimum number of 5 probes per segment were used to call a copy number aberration with significance threshold of 5x10-6. We used log ratio cut offs of ±0.3 to call one copy gain/loss and ±0.7 to call high gain/ homozygous loss.
|
| |
|
| Submission date |
Aug 13, 2013 |
| Last update date |
Dec 17, 2013 |
| Contact name |
Sunita R Setlur |
| E-mail(s) |
ssetlur@partners.org
|
| Organization name |
Brigham and Women's Hospital
|
| Street address |
221 Longwood Avenue
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL10448 |
| Series (1) |
| GSE49827 |
Transformation of the Fallopian Tube Secretory Epithelium Leads to High-grade Serous Ovarian Cancer in BRCA/P53/PTEN Models |
|
