Genome-wide transcriptome profiling of Colon Intestine-Chip and Conventional Organoid Cell Culture System Using RNA-seq

goal of this study was A) to compare global RNA-sequencing (RNA-seq) profiles data of organoid- derived colonic epithelial cells cultured and differentiated in i) conventional suspension organoids cultures (n=3), ii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and stretch (n=4), iii) Colon Intestine-Chips cultured for 5 days under constant flow, without endothelium and with stretch (n=4), iv) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and without stretch (n=4), v) Colon Intestine-Chips cultured for 5 days under constant flow, with endothelium and stretch (n=6), vi) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and stretch (n=4), vii) Colon Intestine-Chips cultured for 8 days under constant flow, without endothelium and with stretch (n=4), viii) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and without stretch (n=4), ix) Colon Intestine-Chips cultured for 8 days under constant flow, with endothelium and stretch (n=3), and B) to identify differences in transcriptome profiles of organoid- derived colonic epithelial cells between following two conditions, unstimulated and basolaterally stimulated with IL-22 (10pM, 100pM or 1nM) Colon Intestine-Chips. Global RNA expression profiles of Colon Intestine-Chip Day 5 cultured without endothelium and stretch (n=4 epithelial channel); Colon Intestine-Chip Day 5 cultured without endothelium and with stretch (n=4 epithelial channel); Colon Intestine-Chip Day 5 cultured with endothelium and without stretch (n=4 epithelial channel); Colon Intestine-Chip Day 5 cultured with endothelium and stretch (n= 6 epithelial channel); Colon Intestine-Chip Day 8 cultured without endothelium and stretch (n=4 epithelial channel); Colon Intestine-Chip Day 8 cultured without endothelium and with stretch (n=4 epithelial channel); Colon Intestine-Chip Day 8 cultured with endothelium and without stretch (n=4 epithelial channel); Colon Intestine-Chip Day 8 cultured with endothelium and stretch (n= 3 epithelial channel)Conventional suspension organoid culture systems Day 0 (n=3 upper compartment); untreated Colon Intestine-Chips (n=3 epithelial channel); treated Colon Intestine-Chips with 10pM IL-22 (n=3 epithelial channel); treated Colon Intestine-Chips with 100pM IL-22 (n=3 epithelial channel); treated Colon Intestine-Chips with 1nM IL-22 (n=3 epithelial channel) were generated by deep sequencing using Illumina HiSeq. Colonic epithelial cells (CoEpiCs).