Ultra-shallow whole genome sequencing of patient sample: Sample UMEL_5_3_usWGS
Excess nuclei (>1x105) from the sample preparations for sn-RNAseq were collected by centrifugation (500 x g, 5 min) and snap frozen after removing all but ~10 µL ST buffer and stored until further processing at -20°C. If insufficient numbers of nuclei were available after loading, additional curls were processed using the same methods as described above for single nuclei extraction. To extract genomic DNA from nuclei the nuclei were briefly thawed on wet ice and genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany; #69504) according to manufacturer instructions and eluted in RNAse and DNAse free water at 37°C for 5 minutes. The DNA concentration was then quantified using a Nanodrop. 20-50 ng genomic DNA served as input for low pass whole genome sequencing (lp-WGS) library preparation with the Lotus DNA Library Prep Kit (Integrated DNA Technologies - IDT, Coralville, IA) using xGen™ Stubby Adapter and UDI Primer Pairs (IDT, #10005921) according to manufacturer instructions.