Illumina HiSeq 1500 paired end sequencing; Bulk RNA-seq of MilliporeSigma 3DGro human patient-derived gastrointestinal organoid lines compared to SCC300 human iPSC-derived colon organoid line
original samples 1-6 were obtained from patient biopsies, expanded and passaged in vitro. Samples 7-8 were derived from induced pluripotent human foreskin fibroblast cells Organoids from Matrigel domes (2 biological replicates per sample)were dislodged and pelleted at 500g for 5 minutes. Supernatant was aspirated and pellets were resuspended in 1 mL TrypLE express using repeated pipetting and incubated at 37 C for 10 min. Samples were pelleted 500g for 5 min. Supernatant was aspirated and resuspended in 400 uL TRI reagent then transferred to a microcentrifuge tube and pelleted 13000g for 10 min. 350 uL supernatant was transferred to a new microcentrifuge tube. Equal volume of 100% ethanol was added and mixed. Samples were column-purified following protocol of Zymo DirectZol RNA miniprep. Poly-A selection was performed on bulk RNA and adapters were ligated for library preparation