Figure 3.

RNA and antibody-based epitope expression in brain infiltrating leukocytes

(A) Example of gating leukocyte populations using CITE antibodies. Briefly, CNS native myeloid cells (microglia and BAM) were gated based on both populations lowly expressing CD45 and then differentiated from each other based on higher I-A-I-E and CD38 expression in BAM. Peripheral leukocytes were gated based on high CD45 expression. Within the peripheral leukocyte population: B cells were defined as having CD19 and B220 expression. T cells were defined based on high CD3 expression and low NK1.1 expression, then subpopulations further distinguished on the basis of CD4 and CD8 expression. Myeloid cells were distinguished from adaptive peripheral immune cells by high CD11b expression, and then further subdivided on the basis of Ly6C expression levels and Ly6G expression.

(B) Example of gating leukocyte populations using CyTOF antibodies.

(C) Biaxial plots of CITE epitope expression on the x axis and its corresponding mRNA expression on the y axis. Discordant expression of mRNA and protein can be observed.

(D) UMAPs derived from CITE-seq data clustered by RNA transcription cluster color coded by transcriptional cluster (left) or canonical cell ID determined by CITE-antibody gating (right). While canonically identified cells generally group within the same cluster, there is appreciable dispersion of canonical cell types among clusters, indicating the utility in using CITE antibody tags rather than mRNA alone to identify canonical cell types.