Barcode sequencing of  mouse mammary tumors
To prepare libraries  for sequencing, DNA concentration was measured using Broad Range Qubit  methodology (Invitrogen). 80 ng of DNA (approximately 12,100 genomes) was  used as input for each single reaction. To increase the number of analyzed  cells we performed 8 reactions per sample; therefore, barcodes from around  97,000 cells were analyzed for each sample. We used a two-step PCR  amplification protocol as described in Lundberget. al.(Lundberg  et al., 2013). In the first step of the reaction barcodes were amplified  using custom primers (Forward: Step1_F, Reverse: Step1_R) for 10 cycles.  KAPA Robust 2G polymerase (KAPA Biosystems-Roche) was used during this step  to ensure efficiency and specificity of barcode amplification. DNA was purified  between steps one and two using magnetic beads at a 1.3(beads):1(reaction)  proportion. During the second step, PCR products from step one were amplified  using custom primers (Forward: ClonalBarcode Adaptor_1, Reverse: PCR  Primer_IndexN) for 23 cycles. KAPA Hifi Polymerase (KAPA Biosystems-Roche)  was used during this step to ensure fidelity of the amplification. DNA was  purified after the second step using magnetic beads at a 1(beads):1(reaction)  proportion. Amplified barcodes were sequenced using custom Clonal Barcodes  R1 sequencing primer and standard TruSeq sequencing primers using an  Illumina HiSeq2500 RapidSingle End 40x9. Custom primer sequences are  shown in Supplemental Table 1 and 2 from Walens et al.