Single-cell cDNA synthesis and amplification

Reverse transcription (RT) and PCR steps were performed as previously described^{66 (link)}. Briefly, SMARTScribe (Takara, 639537) retrotranscriptase, RNAse inhibitor (Takara, 2313A) and a template-switching oligo were added to the cell lysate to perform the retrotranscription step. Immediately after, a PCR mix comprised of SeqAMP (Takara, 638509) and ISPCR primer (binding to a common adapter sequence in all cDNA molecules) was used for the PCR step with 24 cycles of amplification. Target-specific primers spanning patient-specific mutations were also added to RT and PCR steps (Supplementary Table 6a). After cDNA synthesis, cDNA from up to 384 single-cell libraries was pooled, purified using Ampure XP Beads (0.6:1 beads to cDNA ratio; Beckman Coulter) and resuspended in a final volume of 50 μl of EB buffer (Qiagen). The quality of cDNA traces was checked using a high-sensitivity DNA kit in a Bioanalyzer instrument (Agilent Technologies).