Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis
Fig 1
Monitoring proviral replication competence across generations.
(A) Schematic illustrations of the vectors used in this paper. Lavender bars represent the sites of randomized sequence insertions. Features and construction are described in Materials and Methods. (B) Schematic of the experimental flow of the replication competence experiment, depicting the analysis of genomic DNA and viral cDNA harvested from the F1 and F2 generations. Each color represents members of a clone: on initial integration, one cell (represented by a circle) per color. The loss of colors over the course of the experiment represents predicted outcomes of mutational inactivation. (C) Summary of the number of independent zip codes detectable at different stages of the experiment. A total of 63 zip codes were detected in all four pools. The number of clones present at the indicated stage but not later are indicated at the top. (D, E, F) Scatter plots of zip code read proportions across indicated stages of the experiment, as outlined in (B). Each clone is represented by a single point, colored to reflect that clone’s persistence based upon the progression pattern depicted in (C). The Spearman correlation for each comparison is given.