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E-GEOD-40001 - Targeting PyMT oncogene to diverse mammary cell populations enhances tumor heterogeneity and generates rare breast cancer subtypes

Status
Released on 9 August 2012, last updated on 20 August 2012
Organism
Mus musculus
Samples (34)
Array (1)
Protocols (8)
Description
Generating a new mouse model for breast cancer heterogenaity. We use lentiviral infection to integrate the sporatically transforming EF1α-PyMT10C or Muc-PyMT10C into mouse mammary epithelial cell genomes. We then transplant those cells into cleared mammary fat pads of recipient mice, allowing tumors to develop from luminal , myoepithelial, stem and progenitor cell lineages. We developed a wide variety of tumors including rare histologies such as squamous, tubular, spindloid and lipid rich. We used microarray analysis to compare our mouse model with a microarray analysis of 9 established mouse models (Herschkowitz, J.I. et al. Genome Biology, 2007). Heirarchal clustering was used to establish the molecular subtype of tumors developed through the lentiviral-PyMT mouse model. In addition, micrarray analysis was used in conjunction with GeneSifter and GO ontology to identify unique pathways for each of the rare tumor types 43 total microarrays were generated from lentiviral-PyMT tumors, MMTV-PyMT transgenic tumors, and embryonic samples . Nine samples were two color arrays run at UNC microarray facility, while 34 were one color arrays run at Huntsman Cancer Instutite. The two color arrays were treated as one color arrays, we used the Cy3 intensity data for analysis. These data were merged and normalized (quantile and combat) with previously published arrays from UNC. Data were filtered on an intrinsic gene set developed in 2007 (Herschkowitz, J.I. et al. Genome Biology, 2007) and clustered using euclidian distance metrics This GEO submission consists of the 34 one color arrays run at Huntsman Cancer Instutite. The nine two color arrays run at UNC microarray facility are not included.
Experiment type
transcription profiling by array 
Contacts
Bryan Welm <Bryan.Welm@hci.utah.edu>, Brett Milash, Brittni A Smith, Bryan E Welm, Chuck Perou, Collin Keiffer, Dawne Shelton, Phil Bernard
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-40001.idf.txt
Sample and data relationshipE-GEOD-40001.sdrf.txt
Raw data (2)E-GEOD-40001.raw.1.zip, E-GEOD-40001.raw.2.zip
Processed data (1)E-GEOD-40001.processed.1.zip
Array designA-MEXP-724.adf.txt
Links