Fig. 2: Isolation of a target barcoded cell from a complex population.

a, Nucleotide compositions of barcodes prepared for Mammalian CloneSelect Pool-100. Five barcodes with unexpected lengths were excluded from this visualization. The full barcode sequence list can be found in Supplementary Table 1. b, Barcode abundance distribution in the Pool-100 cell population. The pie chart represents the success rate of enriching target barcodes to more than 25% in each sorted cell population. The horizontal blue line shows the least abundant barcode successfully enriched after sorting. c, gRNA-dependent labeling of target barcoded cells in Pool-100 (n = 1). Scale bar, 40 µm. d, Conceptual diagram of the benchmarking experiment using Pool-100. e, Barcode enrichment analysis after the cell sorting of EGFP⁺ cells. Each row shows the barcode abundance profile for the predetermined barcodes in the pool corresponding to each target isolation assay. f, Conceptual diagram of the benchmarking experiment using Pool-10000. Query gRNAs or reporters were individually transfected. The cell samples were pooled later for combined cell sorting and analyzed by high-throughput sequencing. g, Barcoded cell frequencies in pre-sort and post-sort populations (replicate one of n = 2). h, Conceptual diagram representing the separation store of target barcoded cells from a background cell population of similar barcode abundances. i, Separation scores of different isolation attempts from Pool-10000 prepared for different retrospective clone isolation systems. The target barcode abundances were adjusted by the dilution factor introduced by the pooling of different experimental samples. Box plots display the median along with the 25th and 75th percentiles, with whiskers extending 1.5 times the interquartile range. Two-tailed Mann–Whitney U-test was used for statistical analysis; **P < 0.01; ***P < 0.001.