To assess the potential effect of CellTagging on cell physiology we performed scRNA-seq on CellTag-labelled cells and unlabelled control cells 72 h after tagging. a, Left, fluorescent image of CellTag-labelled, GFP-expressing, pre-B cell line, HAFTL-1. Right, 10x Genomics-based scRNA-seq of CellTag-labelled (n = 3,943 cells) and non-tagged control cells (n = 2,067 cells). Cells were clustered using Seurat, resulting in a t-SNE plot with 6 clusters of transcriptionally distinct cells. CellTag-labelled and control cells were evenly distributed across these populations. b, The CellTag-labelled B-cell population expresses a mean of 3.50 ± 0.02 CellTags per cell. c, We detect no observable differences in numbers of genes or UMIs per cell in either population. d, Average gene expression values between CellTag-labelled and control cells are highly correlated (r = 0.999, Pearson’s correlation), demonstrating that our labelling approach does not induce significant changes in gene expression. These experiments were performed independently twice with similar results. e, To assess the potential effect of CellTagging on reprogramming outcome, we induced lineage conversion (MEF to iEP) of CellTagged cells in parallel with unbarcoded control cells, followed by three weeks of culture and processing on the Drop-seq platform (n = 773 cells passing quality control). A mean of 3.30 ± 0.09 CellTags per cell are expressed in a labelled reprogrammed cell population. f, There are no observable differences in numbers of genes or UMIs per cell in either the labelled or unlabelled populations. g, Average gene expression values between CellTagged and control cells are highly correlated (r = 0.98, Pearson’s correlation), again demonstrating that our labelling approach does not induce significant changes in gene expression. h, Seurat clustering of cells, in which cells in fibroblast (Col1a2-high), transition, and fully reprogrammed (Apoa1-high) states can be identified. Right, barcoded and control cells are distributed fairly evenly across these reprogramming stages. Some variation is expected between these independent biological replicates. These experiments were performed independently twice with similar results.