|
| Status |
Public on Mar 01, 2011 |
| Title |
PBC_MMTV-MYC_validation_11 |
| Sample type |
RNA |
| |
|
| Source name |
PBCs from MMTV/c-MYC mice with advanced mammary tumors.
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
genotype/variation: MMTV/c-MYC transgenic
phenotype: tumor-bearing transgenic mouse
tissue: total white blood cells (WBCs)
data set: validation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected using the submandibular (cheekpouch) method. Briefly, the vein that drains the face and cheek area was punctured by a lancet (GoldenRod animal lancet, MEDIpoint, Inc., Mineola, NY) and blood was captured in BD Microtainer™ tubes with potassium-EDTA anticoagulant (Becton Dickinson, Franklin Lakes, NJ). Tubes were immediately inverted 10-12 times and placed on ice.
Following erythrocyte lysis, total RNA was isolated from the leukocyte pellet using the QIAamp RNA Blood Mini Kit (Qiagen, Valencia, CA). Alternatively, the leukocyte pellet was immediately lysed, homogenized and stored at -80°C. RNA was isolated at a later date using the protocol described above or the adapted protocol associated with the QIAamp RNA Blood Mini Kit for use in the QIAcube (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
Purified total RNA (200 ng) was amplified using NuGEN Ovation™ RNA Amplification System (NuGEN Technologies, Inc., San Carlos, CA).
Biotinylated cRNA were prepared according to the standard Affymetrix IVT 1-cycle protocol from 2.5 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.
|
| Scan protocol |
GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).
|
| Data processing |
Data processing was performed in a pilot revision control system entitled Quality-Auditable Data Repository and Analysis (QUADRA). For fully versioned and annotated source code and data objects, please see http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project.
Data were RMA normalized according to the source code found at http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project/human-dataprep.
|
| |
|
| Submission date |
Feb 28, 2011 |
| Last update date |
Mar 01, 2011 |
| Contact name |
Erich Huang |
| E-mail(s) |
erich.huang@duke.edu
|
| Phone |
919-684-6849
|
| Fax |
919-681-8973
|
| Organization name |
Duke University
|
| Department |
Institute for Genome Sciences and Policy
|
| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE27563 |
Expression data from murine PBCs from mice with advanced mammary tumors and their tumor-free counterparts. |
| GSE27567 |
Integrating Factor Analysis and a Transgenic Mouse Model to Reveal a Peripheral Blood Predictor of Breast Tumors |
|
