Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [R9_DAY7.5_10X_genomics]

We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. The regenerative ILCs were detected in multiple tissues including intestine, lung, liver, spleen and thymus. We performed single cell RNA-seq on the sorted GFP+CD45.2+Lin- cells from the bone marrow of recipients at day 7.5 after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative ILC-related progenitors including iLP, iILCP, iILC1/3P and iILC2P, and the cellular trajectory of regenerative ILCs development in vivo was closely resembles the natural ILCs development. Overall design: At day 7.5 after iHPC transplantation, we sorted the GFP+CD45.2+ Lin- cells from the bone marrow of recipients for Droplet-based scRNA-seq. Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture's instruction.