GSM8721056: Targeted barcode sequencing for pre-sort HCC1806 sample, replicate 1; Homo sapiens; OTHER
DNA was extracted from frozen cell pellets containg ~0.5e6 cells using the Invitrogen PureLink Genomic DNA kit (ThermoFisher, K182001) according to manufacturer's instructions. Amplification steps were performed following published ClonMapper barcode amplification procedures (up-to-date web protocol: https://docs.brocklab.com/clonmapper/protocol/, published protocol:https://doi.org/10.1007/978-1-0716-1811-0_8). Briefly, DNA was quantified with NanoDrop, then 1 µg of DNA was loaded into the first PCR reaction. Amplified DNA was cleaned with SPRI beads, then 4 ng of cleaned stage 1 product was loaded into the next PCR reaction to add unique Illumina i7/i5 indices to each sample. Stage 2 samples were cleaned with SPRI beads, then quantified Qubit using the 1X dsDNA high-sensitivity assay (ThermoFisher, Q33231). Illumina indexed samples were run on a NovaSeq 6000 (S1 flow cell, single read, 100 cycles) by the UT Genome Analysis and Sequencing Facility, targeting 100e6 reads for all samples and biasing more reads toward the earlier timepoint samples. ∼14e6 reads were obtained for each initial population, ∼6e6 for each pre-sort sample, and ∼3e6 for each control and fusion sample in each cell line.