Transcriptomic profiles of intestinal stem cells cultured in natural and synthetic three-dimensional matrices

We used RNA-seq to define the gene expression profiles of intestinal stem cells (ISCs) expanded in Matrigel, degradable poly(ethylene) glycol (PEG) and non-degradable PEG matrices. Comparison of mRNA profiles between ISCs grown in Matrigel and non-degradable PEG show no major differences in expression of gene related to stemness, proliferation and signaling via the Wnt and Notch pathways. These results also show that ISC cultured in degradable PEG matrices upregulate stress- and inflammation-related genes compared with cells expanded in non-degradable PEG matrices. Overall design: mRNA profiles of ISCs cultured in the three types of matrices for 4 days were generated in triplicate