Fig. 3: Combined mRNA and epitope profiling from single cells resolves immune cell diversity in the tumor microenvironment.
From: Tracing tumorigenesis in a solid tumor model at single-cell resolution
a Overview of cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) experiments (n = 4). Single live cells were prepared as described earlier. A pool of 63 oligonucleotide-coupled antibodies was incubated with the cell suspension from one submandibular gland, washed and further processed by Drop-seq. The oligonucleotides contain an antibody-specific barcode, a PCR handle and are polyadenylated for capture by the Drop-seq primer beads. b mRNA-based clustering of all single-cell datasets. Cells from the CITE-seq experiments are highlighted (opaque colors) over those from previous ‘Drop-seq only’ transcriptome datasets (translucid colors). c Epitope and mRNA signals in cells from CITE-seq experiments for selected immune-specific markers. d Subclustering of the immune cluster (shown in b) identifies 4 macrophage subpopulations. e Contributions of cells from control or double-mutant samples to immune subpopulations. P-values from mixed effects binomial model using 3207 cells in 30 samples. Boxes span the 25th to the 75th percentile, whiskers 1.5 times the interquartile range.
