GSM6761994: KO1; Mus musculus; RNA-Seq
We followed the protocol published by Corey and coworkers (20) starting from isolated large intestine crypts. Both cytoplasmic and nucleoplasmic RNAs were precipitated and washed with ice-cold 70% (vol/vol) ethanol prior to be dissolved in TriPure reagent (Roche) while the chromatin pellets were immediately dissolved in TriPure. Ten microliters of 0.5 M EDTA was added to all the samples in TriPure that were heated to 65 °C with vortexing until dissolved (~10 min). Colon was isolated from either six EPR fl/fl or six EPR cKO 12-week-old mice and flushed with ice-cold PBS. The proximal third of each colon was excised and immediately frozen in dry ice. Then, the organ fragments were homogenized using a motorized pestle (Sigma-Aldrich) in the presence of TriPure reagent and high-quality RNA was extracted. A total of twelve libraries were prepared using standard Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol and sequenced on Illumina NovaSeq 6000. Image analysis and base calling were performed using the Illumina NovaSeq Control Software.