|
| Status |
Public on Oct 16, 2018 |
| Title |
Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4713-5L-ILC] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mouse Ref cRNA 2ug
|
| Organism |
Mus musculus |
| Characteristics |
reference: total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups.
|
| Treatment protocol |
Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre mice were monitored for tumor progression.
|
| Growth protocol |
Transgenic mouse model
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors frozen in RNAlater (Qiagen 76106) were thawed and homogenized by Qiagen TissueRupter (Qiagen 9001271). RNA was extracted using Qiagen RNeasy mini kit (Qiagen 74104). RNA quantification was determined using the Nanodrop spectrophotometer and RNA quality for microarray was determined using the Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labeled with cyanine-5 (Cy5) dye for tumor samples and cyanine-3 (Cy3) dye for mouse reference samples 51 using the Agilent Low RNA Input Fluorescent Linear Amplification Kit. For both mouse reference RNA and tumor RNA, 2ug of labeled RNA was co-hybridized overnight to Agilent microarrays (platform G4862A).
|
| |
|
| Channel 2 |
| Source name |
B4713-5L-ILC tumor cRNA 2ug.
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary tumor
|
| Treatment protocol |
Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre mice were monitored for tumor progression.
|
| Growth protocol |
Transgenic mouse model
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors frozen in RNAlater (Qiagen 76106) were thawed and homogenized by Qiagen TissueRupter (Qiagen 9001271). RNA was extracted using Qiagen RNeasy mini kit (Qiagen 74104). RNA quantification was determined using the Nanodrop spectrophotometer and RNA quality for microarray was determined using the Agilent Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was labeled with cyanine-5 (Cy5) dye for tumor samples and cyanine-3 (Cy3) dye for mouse reference samples 51 using the Agilent Low RNA Input Fluorescent Linear Amplification Kit. For both mouse reference RNA and tumor RNA, 2ug of labeled RNA was co-hybridized overnight to Agilent microarrays (platform G4862A).
|
| |
|
| |
| Hybridization protocol |
Overnight hybridization to agilent microarray- G4862A.
|
| Scan protocol |
Microarrays were scanned on a Agilent microarray scanner and analyzed using 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 28, 2017 |
| Last update date |
Oct 16, 2018 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
cperou@med.unc.edu
|
| 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 |
GPL24315 |
| Series (1) |
| GSE107432 |
Cdh1 and Pik3ca mutations cooperate to induce Immune-Related Invasive Lobular Carcinoma of the Breast |
|
