Systematic analysis of innate lymphoid cells and natural killer cells in context of HIV-1 infection

We performed bulk and single cell RNA-Seq and ATAC-Seq of CD56-, CD56dim, CD56hi NK cells and innate lymphoid cells, revealed relationship among these developmental related populations, investigated the effect of HIV-1 infection on these innate populations. These findings clarify the interrelatedness of ILC populations disrupted by HIV-1 infection and provide insight into how these functions might be restored. Sorted Lin-CD56-CD127-, Lin-CD56-CD127+, CD56-NK cells (Lin-CD56-CD16+), CD56dimNK cells (Lin-CD56dim), CD56hiNK cells (Lin-CD56hi) and ILCs (Lin-CD56-CD16-CD127+) from CD45+ cells of fresh PBMCs or different culture conditions were subject to bulk-RNA seq (based on CEL-Seq2 protocol), single cell RNA-Seq (based on 10x Genomics instruction, Single Cell 3’ Reagent Kits v2) and ATAC-Seq.