Genome-wide transcriptome profiling of human organoids, colon intestine-chip and human alveolus-chips using RNA-seq

The goal of this study was to compare RNA expression of the A) CEA gene obtained from i) colon intestine organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Colon Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human colon intestine tissue and to verify whether Colon Intestine-Chip faithfully recapitulates human duodenum tissue and to better understand how much it differs from the organoids from which it's derived, and B) FLOR1 gene obtained from i) human alveolar epithelial cells in T-25 Flasks, ii) human Alveolus Lung-Chip on day 5 and day 10 of the culture. Overall design: Global RNA expression profiles of colon intestine organoids (Organoids; n=3); Colon Intestine-Chips derived from organoids (Colon Intestine-Chip; n=3); Alveolus epithelial-cells Day 0 (n=3); Alveolus Lung-Chip Day 5 (n=3); Alveolus Lung-Chip Day 10 (n=3) were generated by deep sequencing using Illumina HiSeq 4000.