GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE40001 Query DataSets for GSE40001
Status Public on Aug 10, 2012
Title Targeting PyMT oncogene to diverse mammary cell populations enhances tumor heterogeneity and generates rare breast cancer subtypes
Organism Mus musculus
Experiment type Expression profiling by array
Summary We are generating a new mouse model for breast cancer heterogenaity using lentiviral infection to integrate the sporatically transforming EF1α-PyMT10C or Muc-PyMT10C lentivirus 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.
Overall design 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 Cy5 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.
Contributor(s) Smith BA, Shelton D, Keiffer C, Milash B, Perou C, Bernard P, Welm BE
Citation Brittni A. Smith, Dawne N. Shelton, Collin Kieffer, Brett Milash, Jerry Usary, Charles M. Perou, Philip S. Bernard and Bryan E. Welm. Targeting the PyMT Oncogene to Diverse Mammary Cell Populations Enhances Tumor Heterogeneity and Generates Rare Breast Cancer Subtypes. Genes & Cancer OnlineFirst, published on January 29, 2013 as doi:10.1177/1947601913475359
Submission date Aug 09, 2012
Last update date Jan 12, 2017
Contact name Bryan Welm
Phone 801-587-4633
Organization name University of Utah, Huntsman Cancer Institute
Department Oncological Science
Lab Bryan Welm Lab
Street address 2000 Circle of Hope Drive
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
Platforms (1)
GPL7202 Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version)
Samples (43)
GSM983136 Tumor_10_HCI
GSM983137 Tumor_17_HCI
GSM983138 Tumor_21_HCI
BioProject PRJNA172249

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40001_RAW.tar 388.9 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap