Extended Data Fig. 1: CBL model selections, signal amplification and plasmid capture.

a, Cells expressing RT521K were spiked into an excess of cells expressing inactive RT (RT-ΔDTD) at 1:100 (top) and 1:1000 (bottom) ratios and encapsulated in w/o emulsion with beads coated with DNA primer bbFd and template TnotTest7 (Supplementary Table 7). After in-emulsion cell lysis and primer extension, beads were recovered and sorted for fluorescence using FACS (middle panel, dashed box). Plasmids recovered from sorted beads were amplified by qPCR and the amount of RT521K and RT-ΔDTD plasmids post-CBL selection quantified. Enrichment was calculated by determining the ratio of RT521K: RT-ΔDTD plasmids in the input (before CBL selection) (left panels) and comparing it with the output ratio (after CBL selection)(right panels) yielding enrichment factors of ~500-fold in both cases. b, HCR signal amplification. Cells expressing RT521K were encapsulated with beads coated with primer bbTest7 annealed to RNA template tnog_full (Supplementary Table 7) and RNA reverse transcription was performed in emulsion. After recovering the beads from emulsion, the sample was split in half and beads were treated with either a nucleic acid probe (top bead) or underwent HCR (bottom bead). Flow cytometry analysis of the beads labelled with a direct probe (top plot) or HCR (bottom plot) shows approximately an order of magnitude increase in signal and a greater percentage of fluorescently labelled beads in HCR conditions. c, Plasmid capture on microbeads. Plasmids bound to beads during CBL were quantified by qPCR. Cells expressing RT521K were combined with beads in bulk (in solution) or were encapsulated in w/o emulsions and underwent reverse transcription. Beads in w/o emulsion were extracted and bulk and emulsion treated beads were sorted for fluorescence by HCR. The number of plasmids per bead was quantified before and after FACS. Purified plasmid was bound to beads without capture oligo (untreated beads) and with capture oligo as controls showing approximately 10 plasmids captured per bead in emulsion and stably bound (surviving post-sort).