Extended Data Fig. 8: Single-cell RNA-seq points to the exclusion of markers of T cell activated state from HIV-infected cells.
From: HIV infection reprogrammes CD4+ T cells for quiescence and entry into proviral latency
a-d. UMAP projection of single-cell RNA-seq data shows that cells with high levels of cellular activation markers CD25 and CD71 (a, b) and metabolic markers GAPDH and LDHA (c, d) are found predominantly among uninfected and reactivated HIV+ cell clusters, consistent with the lower proliferation and metabolic activity in +HIV 96 hpi and quiescent cells. e. The total number of UMIs (unique molecular identifiers) per cell, which is an indirect measure of cell size and total number of cellular transcripts, is shown for cells in each category. A smaller value is associated with quiescence in T cells. In this panel and f, the shown data is obtained from single-cell RNA-seq on a healthy donor, and in each violin plot, the central box indicates the interquartile range (25th–75th percentile), the white dot within the box marks the median, and the whiskers extend to 1.5× the interquartile range. f. Dual activation of p53 and KLF2 signaling leads to the lowest proviral transcriptional activity even when the HIV counts (UMIs) in each cell are normalized to total counts (UMIs) per cell.
