a, FACS plots demonstrating the gating strategy used for sorting. The population sorted for scRNA-seq is indicated in red. b, Heat map of gene expression for cellHarmony-assigned cell populations from CITE-seq 10x Genomics captures (male and female mice, n = 11,132 cells) compared with ICGS-defined clusters from the Fluidigm scRNA-seq data. De novo marker genes (MarkerFinder) for each assigned cluster from the 10x Genomics data are shown (top). Each column represents a single cell and each row represents a single gene. Multi-Lin*, multi-lineage primed. The gender of the host mouse of each cellular barcode (bottom) and example MarkerFinder genes in common between Fluidigm and 10x Genomics data are indicated (right). c, Violin plots of the gene and read-level metrics for each of the indicated libraries. Dashed lines indicate mean, lower, and upper quartiles. Sample size (n = number of cells) displayed (top). d, Lineage-priming scores for monocytic and granulocytic specification. Scatter plot displaying assigned scores for cellHarmony-assigned neutrophil progenitors (proNeu-2), monocytic progenitors (Mono), bi-potential monocytic–granuloctyic intermediates (IG2) and megakaryocyte progenitors (Meg) from b (see Methods). Each point represents a single cell. e, Heat map of row-normalized ADT UMI counts (log 2 -transformed, median subtracted) for each corresponding cell from b. f, Heat map of cell cycle gene expression displaying the same cells as b and the same genes as Extended Data Fig. 4h. g, Scatter plot representation of scRNA-seq data from f comparing the gene expression of G1-to-S phase transition genes with G2-to-M phase transition genes in each cell. Each point represents a single cell. h, Bar chart of the heat map in b, displaying the incidence and amplitude of selected genes. i, Heat map of correlation between gene expression and each displayed cluster as generated by the MarkerFinder feature of AltAnalyze. j, k, Plots of CITE-seq ADT UMI counts, in which grey indicates all captured cells, and red indicates either cells classified by ICGS clusters (j) or the top 1% of UMIs expressing the indicated gene (k). l, UMAP of 15,968 published cell-barcodes23 coloured according to cellHarmony assigned cell populations (10x Genomics reference) where each dot represents a single cell. Minor contaminant populations (<30 cells per cluster) were excluded. m, Heat map of row normalized CLR-transformed ADT counts of the indicated cell surface proteins (left) displayed as an average of all cells in the indicated clusters (top). n, Correlation plots between ADT UMI counts and the expression of genes (cellular barcode normalized UMI counts) encoding the corresponding proteins detected via CITE-seq. Each dot represents a single cell. Linear trend lines for all cells with RNA expression > 0 are indicated by dotted red lines with corresponding coefficients of determination displayed. Data in i display Pearson correlation values. Source Data