CD4 and infection: To determine the reproducibility and generality of our findings, we used multiple independently performed RNA-seq studies involving early HIV infection timepoints from public databases (Supplementary Table 1) in which high levels of infection were achieved using different strains of replication-competent HIV from LAI and NL4-3 clones39,41,43,46,47 and primary HIV isolates42,44, which were used to infect diverse CD4+ T cell lines and primary CD4 cells (Supplementary Table 1).