title: NextSeq 500 sequencing; Culture associated DNA methylation changes impact on cellular function of Human Intestinal Organoids (Expression)
design: Culture associated DNA methylation changes impact on cellular function of Human Intestinal Organoids (Expression)
library_construction_protocol: Human IEO were generated from mucosal biopsies by isolation of intestinal crypts and culturing in Matrigel® (Corning) IEO were cultured for 5 days after splitting in the growth medium, followed by 24 h treatment with recombinant human protein TNFα (H8916, Sigma Aldrich) at 40 ng/ml or IFNγ (PHC4031, Life Technologies) at 20 ng/ml.  At the end of each experiment, human IEO were harvested and both DNA and RNA were extracted using the AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany).  RNA was prepared with the Truseq mRNA library preparation (Illumina, San Diego, CA, USA)