title: Illumina HiSeq 2500 paired end sequencing; Soluble Guanylate Cyclase Signalling Mediates Etoposide Resistance in Progressing Small Cell Lung Cancer
library_construction_protocol: Genomic DNA was extracted from flash frozen CDX tumours using the DNeasy Blood and Tissue kit (Qiagen, 69504) by incubating tissue overnight (O/N) in buffer ATL with proteinase K at 56˚C. Genomic DNA was quantified using a Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854) and run on the Agilent Tapestation Genomic DNA assay (Agilent, 5067-5365).  ). Genomic DNA was sheared on the Bioruptor Pico sonication system (Diagenode, B01080010) to an average size of 150-200 bp. Libraries were prepared using 200 ng of sheared genomic DNA, 10 cycles of pre-capture PCR and 11 cycles of post-capture PCR, with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing (Agilent, G9641B). Low input samples were prepared using 8 - 200 ng of sheared genomic DNA, eight - 11 cycles of pre-capture PCR and nine cycles of post-capture PCR, with the SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing (Agilent, G9703A).  SureSelectXT Human All Exon V6 Capture Library (Agilent, 5190-8865) was used for all samples. Library quality was checked using the Agilent Bioanalyzer. Libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina (Roche, 07960336001).