Fig. 1

Single-cell RNA sequencing of milk and blood cells from cattle with chronic mastitis reveals six major cell types. (A–C) t-SNE plots showing sample origin (A), cluster assignment (B), and cell type annotation (C) of cells recovered via scRNA-seq. (D) t-SNE plots showing expression of a subset of canonical genes used to annotate cell types shown in (C). (E) Dot plot of canonical genes (x-axis) used to annotate clusters into cell types (y-axis). Dot size within the plot indicates the percentage of cells in a cluster expressing a gene. Dot fill color indicates the relative expression level of a gene in a cluster. The color bar on the left of the y-axis indicates cell type assignment of clusters. (F) t-SNE plots showing number of UMIs (top) or number of genes (bottom) expressed in each cell. In all t-SNE plots (A–D,F), each dot in the plot corresponds to an individual cell. Color of each dot in a plot corresponds to assignment of a cell to sample origin (A), cluster assignment (B), cell type annotation (C), level of gene expression (D), or number of UMIs or genes recovered from a cell (F). Proximity of cells within a plot is not necessarily a correlate of relatedness. *Gene name is not listed in the genome annotation file but was identified through manual query. See methods section “Gene name replacement” for further information. ASC antibody-secreting cell, cDC conventional dendritic cell, ILC innate lymphoid cell, pDC plasmacytoid dendritic cell, scRNA-seq single-cell RNA sequencing, t-SNE t-distributed stochastic neighbor embedding, UMI unique molecular identifier.