Fig. 1: ASAPseq identification of HIV-infected cells in vitro.
From: Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4+ T cell reservoir
a, UMAP representation of ATAC component colored by manually annotated cell phenotypes. b, UMAP representation of ATAC component colored by detection of HIV reads. c, Absolute count of cell numbers based on annotated clusters. d, Percentage of HIV+ cells found in each annotated cluster. e, Differential expression of surface antigens was assessed (DESeq2 method in Seurat; two-sided with multiple comparison adjustment using the Bonferroni–Hochberg method) between activated HIV+ cells (n = 1,040) and activated HIV– cells (n = 1,194). Positive fold change (FC) values indicate higher expression in HIV+ cells, whereas negative FC values indicate higher expression in HIV– cells. Activated cells are defined as the combination of CD4 activated/effector, CD4 activated 1, and CD4 activated 2 clusters. Markers are arranged from top to bottom by π-score, which is defined as (–log10(FDR) × log2(FC)). All markers shown have an adjusted P value (Padj) <0.05.
