High-resolution retrospective single cell lineage tracing with mutable homopolymers

We present a single-cell dual-omic method (RETrace2) for simultaneous lineage tracing and cell-type identification. In a microsatellite-unstable mouse model, RETrace2 can trace lineage continuously at a resolution close to 5 cell divisions. This was accomplished using homopolymers as markers that are ~2x more informative than other repeats, plus protocol optimizations to improve target capture and reduce experimental errors. We validated RETrace2 in vitro and demonstrated in vivo cell lineage construction of brain, kidney and liver from MSH2 mutant mice.