a, The CellTagging workflow: a lentiviral construct contains an 8-bp random CellTag barcode in the 3′ untranslated region (UTR) of GFP, followed by an SV40 polyadenylation signal. Transduced cells express unique combinations of CellTags, resulting in distinct, heritable signatures, enabling tracking of clonally related cells. b, Representative CellTag expression in two clones, defined by unique combinations of three CellTags (n = 10 cells per clone). c, Left, overlap of individual CellTags in two independent biological replicates tagged with the same CellTag library. Right, CellTag signatures are not shared between the two replicates (replicate 1, n = 8,535 cells; replicate 2, n = 11,997 cells). d, Experimental approach: MEFs are tagged with the CellTagMEF library, expanded for two days and then split for cell fate reprogramming in two independent biological replicates. Additional CellTagging was performed at 3 days (CellTagD3) and 13 days (CellTagD13) after initiation of reprogramming. Every 3–7 days, a sample of cells was collected for scRNA-seq, and the remaining cells were cultured. e, Visualization of scRNA-seq data. Projection of time points and CellTag expression onto a t-SNE plot (time courses 1 and 2, n = 85,010 cells). f, Scoring single-cell identity via quadratic programming. Cells scoring >0.75 (upper red line) are classified as iEPs; cells scoring <0.25 (lower red line) are classified as fibroblasts (n = 85,010 cells). g, Left, projection of identity scores onto the t-SNE plot. Right, designations of t-SNE clusters: fibroblast, early transition, transition and reprogrammed.