Transposase-based DNA Library Preparation

Up to 50,000 cells per sample were tagmented with Nextera Tn5 transposase using the Illumina Nextera kit and purified with a Qiagen MinElute reaction kit per methods modified from Buenrostro et al. (2013) (link). The DNA was then PCR amplified to add indexing primers in nine cycles. SPRI AMPure beads enriched for fragments under ∼600 bp. The library was then amplified again with the nine-cycle protocol, followed by cleanup with SPRI AMPure beads. The DNA library was quantified with a Qubit DNA High Sensitivity assay and analyzed for quality and size distribution on an Agilent 2200 TapeStation with a High Sensitivity D5000 ScreenTape. Samples were pooled at a 10 nM final concentration. Sequencing was run with an Illumina HiSeq 2500 system with 2 × 50 bp read length by the Washington University in St Louis School of Medicine GTAC.