RNA-seq of human intestinal organoids colonized with E. coli and other immature intestinal tissues. RNA-seq of human intestinal organoids colonized with E. coli and other immature intestinal tissues

We performed RNA-seq to demonstrate that the epithelium of human pluripotent stem cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. RNA was isolated using the mirVana RNA isolation kit and following the \"Total RNA\" isolation protocol (Thermo-Fisher Scientific, Waltham MA). RNA library preparation and RNA-sequencing (single-end, 50 bp read length) were performed by the University of Michigan DNA Sequencing Core using the Illumina Hi-Seq 2500 platform. Transcriptional quantitation analysis was conducted using 64-bit Debian Linux stable version 7.10 (\"Wheezy\"). Pseudoalignment of RNA-seq data was computed using kallisto v0.43.0 and differential expression of pseudoaligned sequences was calculated using the R package DEseq2.