D5000 screentape assay

To obtain enough DNA for sequencing from each cell, we carried out single-cell whole genome amplification (scWGA) with the Ampli1 Kit (Menarini Silicon Biosystems, Italy). To avoid contamination, we worked under a biological safety cabinet, UV-irradiated all the plastic materials employed, and used a dedicated set of pipettes. In addition to the patient cells, we included a positive (10 ng/µl REPLIg human control kit, QIAGEN, Netherlands) and negative (DNase/RNase free water) control in the amplification process. We assessed the quality of the amplified DNA with the Ampli1 QC Kit. For positive samples for the four Ampli1 QC PCR fragments, we used the Ampli1 ReAmp/ds kit to increase the amount of total double-stranded DNA. After this, we removed the kit adaptors adding 5 µl of NE Buffer 4 10X (New England Biolabs, MA, USA), 1 µl of MseI 50U/µl (New England Biolabs, MA, USA), and 19 µl of nuclease-free water to every 25 µl of sample and incubated this mixture at 37ºC for 3 h, followed by 20 minutes at 65ºC for enzyme inactivation. After incubation, we purified the samples using 1.8X AMPure XP beads (Agencourt, Beckman Coulter, CA, USA). Finally, we measured the DNA yield with a Qubit 3.0 fluorometer (Thermo Fisher Scientific, MA, USA) and the amplicon size distribution with the D5000 ScreenTape assay in a 2200 TapeStation platform (Agilent Technologies, CA, USA).