DNA library preparation of microdissected tissue samples was undertaken as previously described, using a bespoke low-input enzymatic-fragmentation-based library preparation method28 (link),29 (link),31 (link),66 . This method was employed as it allows for high-quality DNA library preparation from a very low starting quantity of material (100–500 cells). DNA library concentration was assessed after library preparation and used to guide the choice of samples to take forward to DNA sequencing. Minimum library concentration was 5 ng µl–1, and libraries with >15 ng µl–1 were preferentially chosen; 150-bp, paired-end Illumina reads were prepared with Unique Dual Index barcodes (Illumina).
DNA sequencing was undertaken on a NovaSeq 6000 platform using the XP kit (Illumina). Samples were multiplexed in pools of 6–24, then sequenced to achieve a coverage of ≥30×.
DNA sequencing was undertaken on a NovaSeq 6000 platform using the XP kit (Illumina). Samples were multiplexed in pools of 6–24, then sequenced to achieve a coverage of ≥30×.
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