tumor collection protocol: Spontaneous C57Bl/6 PyVmT tumors 0.8-1cm in diameter were dissected and stored frozen at -80°C until RNA isolation procedures. tumor collection protocol: Tumor cells from various C57Bl/6 PyVmT-derived clonal cell lines were injected at 10^6 cells in 2 mg/ml matrigel into the abdominal mammary fat pads of female C57Bl/6 mice. At 6-8 weeks, tumors 0.8-1cm in diameter were dissected and stored frozen at -80°C until RNA isolation procedures. In some cases tumors were enzymatically digested and cell suspensions reinjected into the mammary fat pads of new syngeneic recipients. Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the UCSD (University of California, San Diego, La Jolla, CA, USA).
Label
Cy3
Label protocol
Labeling was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI, USA standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.
Description
LE41 This sample is of a Py15-4 cell line-derived mammary tumor. Py15-4 was derived from the Py230 cell line. It is the second tumor used in this experiment, each from independent animals.
Data processing
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).