Single-cell ATAC-seq integrative investigation revealing comprehensive characteristics of HIV-1-infected cells

To comprehensively reveal the characteristics of the cells infected with human immunodeficiency virus type 1 (HIV-1), GFP-expressing HIV-1 was inoculated into a human hematopoietic stem cell-transplanted humanized mouse model. Infected cells (i.e., GFP-positive cells) and uninfected cells (i.e., GFP-negative cells) were respectively sorted and were used for single-cell ATAC-seq analyses. Additionally, CD4+ T cells that were isolated from the mock-infected mice were also analyzed. The single-cell capture, cell lysis, and ATAC reaction was performed with Fluidigm C1 system. Prior to cell lysis on the C1 System, the capture site was checked whether it contains a single alive cell. The sequence library was constructed with Nextera XT DNA library preparation kit. The 36-bp single-ended sequencing was performed with illumina HiSeq2500.