Illumina HiSeq 2500 paired end sequencing; Soluble Guanylate Cyclase Signalling Mediates Etoposide Resistance in Progressing Small Cell Lung Cancer
Soluble Guanylate Cyclase Signalling Mediates Etoposide Resistance in Progressing Small Cell Lung Cancer
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).