Multi-omics study of Indian ovarian cancer samples
To prepare libraries for Whole Exome Sequencing, 100ng-1g of genomic DNA was sheared with the Covaris S220 (Covaris, Woburn, MA, USA), followed by end-repair, 3 end Adenylation and ligation with paired-end adaptors. Post ligation, 15l of the purified libraries were PCR amplified, all the above steps were performed using the Agilent SureSelectXT kit and every step was followed by DNA purification on a magnetic stand using AMPure XP Reagent beads (Beckman Coulter Genomics, Danvers, MA, USA). Afterward, size (approx 225-275 bp) and quantity (>800ng) were verified employing the Agilent Tapestation 2200 system followed by hybridization and probe capture using Exome SureSelect Human All Exon V6+UTR probes (Agilent). Dynabeads MyOne Streptavidin T1 magnetic beads (Thermofisher). Finally, Captured Libraries were amplified with 12 cycles of PCR using indexing primers containing 8-bp indices, followed by an amplification using AMPure XP beads (Beckman Coulter). Final libraries were checked for quality (each fragment size approx. 300-400 bp) and quantity using Agilent Tapestation 2200 system