Hybridization to Whole Human Genome 4x44k Microarrays (Agilent) was performed by the Genome Technology Access Center (GTAC) at Washington University – St. Louis.
Cy5 labeling with the ULST Fluorescent Labeling kit (Kreatech)
Formalin-fixed paraffin-embedded tissue sections (5 uM) were prepared from the set of archived surgical resection samples used for histological analysis in this study. Whole ileal material was procured by scraping two tissue sections per sample (n = 40). Laser capture microdissection (LCM) was performed using the Arcturus system and CapSure HS LCM caps (Applied Biosystems); methyl green stain was used to identify Paneth cells (~8,000 Paneth cells were microdissected per sample; n = 15). RNA extraction was performed using the RNeasy FFPE kit (Qiagen) followed by cDNA synthesis and amplification with the Transplex Whole Transcriptome Amplification kit (Sigma) and purification with the PCR Purification kit (Qiagen) according to the manufacturers instructions.