Enhancing single-cell cellular state inference by incorporating molecular network features

Although small intestine epithelium has been studied widely in murine, a comprehensive expression landscape in human is still lacking. To explore the cellular diversity of human small intestine epithelium, we sampled the ileal crypts from two patients suffered from right-sided colon cancer while their ilea were relatively normal. scRNA-seq libraries were generated using the 10X v3 Kit, which could guarantee both throughput and quality Using 10X Genomics v3 Kit, we generated a human adult ileal scRNA-seq dataset, where identified several novel stem/progenitor clusters, including a Cripto-1+ cluster. Moreover, two distinct groups of goblet cells were identified and only one of them tended to secrete mucus. Besides, we found that the recently identified BEST4+OTOP2+ microfold cells also highly expressed CFTR, which is different from their colonic counterparts.