Extended Data Fig. 3: Validation of EPI-clone’s capability on a biological replicate (experiment M.2).

a,b,c. Clonal UMAP based on static CpGs as in Fig. 2b, computed for experiment M.2: LARRY replicate experiment. Indicated are the cell state (A) and the LARRY barcode (B). C highlights cells that were selected as part of expanded clones, based on local density in PCA space. d. Receiver-Operating Characteristics Curve characterizing the performance of the local density criterion in selecting expanded clones for the biological replicate. e. Overlap between clones defined using EPI-clone and ground truth labels for the biological replicate. The remark ‘small clones’ indicates all LARRY clones with a relative size less than 0.25%. f. Same UMAP as in Fig. 2b highlighting the LARRY donor labeled by two unique fluorophore sequences. For experiment M.1, two donor mice were sacrificed and HSCs were labeled with LARRY constructs containing a GFP label in one case, and LARRY constructs containing a Sapphire label in the other case. Subsequently, labeled cells from each donor were transplanted into two recipient mice each. Accordingly, the data set contains cells from four mice that contain two sets of clones, labeled with GFP and Sapphire, respectively, see also methods. g. Comparison between the performance of the density-based clustering of EPI-Clone with the performance of CHOIR⁴⁴, a parameter-free clustering method. Precision and recall were calculated for the identification of cells from expanded (>0.25%) clones. ARI: Adjusted rand index. The results are shown for experiment M.1: LARRY main experiment.

Source data