title: Illumina HiSeq 4000 sequencing; RNA seq of a pancreatic cancer patient-derived xenografts treated with Vehicle or Gemcitabine/Paclitaxel in mouse
design: RNA seq of a pancreatic cancer patient-derived xenografts treated with Vehicle or Gemcitabine/Paclitaxel in mouse
library_construction_protocol: PDX13 was established from surgically resected tumor tissue from an adult pancreatic ductal adenocarcinoma (PDAC) patient at the Ruhr-University Bochum Comprehensive Cancer Center. Informed and written consent was obtained. Approval by the ethics committee of the Ruhr University Bochum was obtained under Permission no. 3534-9, 3841-10, 16-5792. Experiments were performed according to the guidelines of the local Animal Use and Care Committees at the Ruhr University Bochum (8.87-50.10.32.09.018, 84-02.04.2012.A328  and 81-02.04.2017.A423). Tumor tissues was implanted in NMRInu/nu mice (both flanks). Tumors were expanded and re-implanted for at least three generations. Later, 1-2mm of tumor tissue (early passage) were implanted subcutaneously in 5–10-week-old mice (NMRInu/nu). Treatment was started when tumors were approximately 100-200 mm3 in size. Mice were randomized into vehicle (09.% saline) or Gemcitabine/Paclitaxel  (100/30 mg/kg). The integrity of RNA was validated by gel electrophoresis and 500ng were used to make the libraries in triplicates for each condition. RNA was extracted using Trizol Libraries for cells were made using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer's instructions.