Projecting cellular immunophenotypes onto Drop‐seq data Projecting cellular immunophenotypes onto Drop‐seq data Schematic to generate scRNA‐seq data using index‐enabled FACS sorting into 96‐well plates, and to project this data onto the Drop‐seq hierarchy to evaluate surface marker expression.Compositional makeup of SMART‐Seq2 experiments, after projection onto Drop‐seq data (Materials and Methods). Height of each bar segment indicates the percentage of cells that map to each Drop‐seq annotation. To facilitate visual comparison, the background distribution of all CD34+ cells is shown three times.Distribution of indexed protein levels for CD52 (top) and CSF3R (bottom) for cells mapping to three Drop‐seq branches. Protein expression is shown in log‐scale. **P < 10−3, *P < 0.05 (Kolmogorov–Smirnov test).We observe a significant (P < 10−3; Welch two‐sample t‐test) relative depletion of lymphoid progeny (CD19+ B cells and CD56+ NK cells) from CD52− CSF3R+ progenitors, compared to CD52+ CSF3R− progenitors after in vitro differentiation with the MS5‐MBN assay. Barplot shows results from three separate cord blood units (error bars reflect SE based on all replicates within each unit, which range from two to five depending on total cell number). Shiwei Zheng et al. Mol Syst Biol 2018;14:e8041 © as stated in the article, figure or figure legend