7 μM sections from formalin-fixed, paraffin-embedded (FFPE) tissue blocks were cut and mounted on PEN membrane slides (Thermo Fisher LCM0522). Slide was dissected immediately after staining on an Arcturus XT LCM System (Thermo Fisher A26818). The cells in different regions were separated and adhered to CapSure HS LCM Caps (Thermo Fisher LCM0215). Genomic DNA was isolated from these different caps using PicoPure DNA Extraction kit (Thermo Fisher KIT0103). 50 μL lysis buffer with proteinase K were added into each sample and incubated at 65°C overnight. After inactivating proteinase K at 95°C for 10 mins, the genomic DNA was cleaned up with AMPure XP beads at 3:1 ratio (Beckman Coulter A63880) and eluted in the 10 mM Tris-HCl (pH 8.0). The DNA concentration was measured by Qubit® dsDNA HS Assay Kit (Thermo Fisher Q32851).
sgID-BC amplicon libraries were prepared from genomic DNAs by single-step PCR amplification with NEBNext Ultra II Q5 Master Mix (M0544L) using dual indexing primer pairs. PCR products were purified first using MinElute PCR Purification Kit (Qiagen 28006), then with Agencourt AMPure XP beads (Beckman Coulter A63881) and assessed for quality with Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer prior to sequencing on the Illumina MiSeq Nano platform (Admera Health Biopharma Services).
sgID-BC amplicon libraries were prepared from genomic DNAs by single-step PCR amplification with NEBNext Ultra II Q5 Master Mix (M0544L) using dual indexing primer pairs. PCR products were purified first using MinElute PCR Purification Kit (Qiagen 28006), then with Agencourt AMPure XP beads (Beckman Coulter A63881) and assessed for quality with Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer prior to sequencing on the Illumina MiSeq Nano platform (Admera Health Biopharma Services).