Temporal transcriptome profiling of chicken (Gallus gallus) enteroids

Enteroids are miniature self-organising three-dimensional (3D) tissue cultures which replicate much of the complexity of the intestinal epithelium. Transcriptional profiling of chicken embryonic intestinal villi and chicken enteroid cultures using bulk RNA-seq was conducted. Culture consistency and stability is demonstrated through comparison of biological and technical replicates, confirming the reproducibility of enteroid-based experiments. The temporal expression of numerous cell subpopulation and function markers indicates that these in vitro intestinal models differentiate from late embryonic intestinal villi to recapitulate many of the digestive, immune and gut-barrier functions seen in vivo post-hatch. Transcriptional changes notable in later cultures provide insight into interventions that may contribute to longer term viability of apical-out cultures. We comprehensively characterised the expression profiles of chicken enteroids at different stages of culturing in comparison to the in vivo chicken gut. This submission contains RNA-seq data from days 1 and 4; for days 0, 3 and 7 see project PRJEB37491.