DNA-seq of H. sapiens: pancreatic cancer patients
Genomic DNA was isolated from archival formalin-fixed paraffin embedded (FFPE) blocks using RecoverAll Total Nucleic Acid Isolation Kit (Ambion/Thermo Fisher Scientific). First layer of tumor blocks was discarted and the remaining sample was macrodissected. In total, eight 10um thick sections were cut from each block. 500 ng of DNA was fragmented to an average size 200 bp using Covaris M220 instruments with the following setting: Temperature 6C, Peak incident power 75, duty factor 10, cycles per burst 200, treatment time 660s. Libraries were prepared using KAPA Library Preparation Kit for Illumina platforms. Target enrichment was performed by the SeqCap EZ Choice (Nimblegen/Roche) using a standard SeqCap protocol with the modifications recommended for FFPE samples (Raterman et al. Roche Diagnostics GmbH, 2013).