Name: HPAXF049
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: In-house PDX models were established from fresh patient tissue procured from Maine Medical Center BioBank (Portland, ME) and consented according to the Human Biological Samples Policy. Samples were received within 24 hours of surgery, minced and implanted subcutaneously into either NSG or CB17 SCID mice. The HBXF-079 sample was implanted orthotopically. The CTC-174 model was developed from circulating tumor cells in patient blood samples procured from Conversant Biologics (Huntsville, AL) and consented according to the Human Biological Samples Policy. The cells were isolated and implanted into the mammary fat pad of NSG mice. In addition, several models were purchased from Jackson Laboratories (Sacramento, CA) as tumor-bearing NSG mice. In most cases, the models were serially transplanted into fresh NSG mice as fragments for expansion and characterization, except BR0869F. For the remaining models, small pieces of PDX derived tumor were purchased specifically for profiling from Experimental Pharmacology and Oncology (EPO; http://www.epo-berlin.com), Xentech (http://www.xentech.eu) and Champions (http://championsoncology.com) representing athymic nude, SCID, or NSG mice. ~50mg of tissue were cut from the frozen tumours and RNA isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to manufactureras instructions. On-column DNase digestion was performed using the RNase-free DNase Kit (Qiagen). RNA concentration was measured using the NanoDrop ND1000 (NanoDrop), and quality determined using the Agilent RNA nano 6000 kit and Bioanalyzer (Agilent Technologies). RNA integrity numbers (RIN) for all samples fell between 7 and 10. Illumina TruSeq Unstranded