Instrument: Illumina HiSeq 3000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: For transcriptome (RNASeq/RefSeq) analysis , ileum from each WT, Casp8–/–Ripk3–/– and Casp11-negative mouse (5 male mice per group) harvested at 1.5 hpc was placed in RNAlater (Thermo-Fisher) at 4C. 24 h post-harvest, intestines were cleaned with cold RNAlater and mucus was scraped, homogenized and pelleted as described for immunoblot analysis. RNA isolation and further steps for transcriptome analysis were carried out as described (Sandler et al., 2014) in the NHP Genomics Core, Yerkes National Primate Research Center. Briefly, total RNA was isolated from mucus pellet for each sample using RNeasy Micro and RNA integrity was tested using Agilent Bioanalyzer capillary electrophoresis. cDNA libraries were prepared using Illumina Stranded RNATruSeq kits and barcoded as well as sequenced on an Illumina HiSeq 3000. Five million 150-base pair mapping reads were obtained per sample, with >90% reads having Q-Scores of >30 (>99.9% estimated accuracy for 150 base reads).