scRNA-seq for E16.5 intestinal epithelial cells grown in conventional organoid cultures or as engineered tissues

As part of our characterization of cellular complexity within our in vitro cultures, we performed scRNA-seq experiments analysing mouse E16.5 intestinal epithelial cells cultured 1) in conventional organoid cultures 3D or 2) as engineered tissues on microfabricated hydrogel scaffolds. We identified 6 transcriptionally disting clusters of both, fetal and adult identity highlighting the cellular complexity within our in vitro models. Overall design: Four samples containing 2 biological replicates from 3D cultures and two biological replicates from engineered tissues were collected, subjected to cell sorting and tagged using hashtag oligos. Subsequently, samples were pooled and sequenced with Illumina NovaSeq 6000 platform.