GSM4973561: HHDST 2358; Sus scrofa; RNA-Seq
Colonic mucosa was homogenized and RNA was isolated using TRI reagent. Isolated RNA was treated with Turbo DNase (Ambion, Waltham, MA) to minimize genomic DNA contamination. RNA quality was assessed using the Experion RNA analysis electrophoresis kit (Bio-Rad, Hercules, CA). Only samples with an RNA Quality Indicator (RQI) greater than 8 were sequenced. Prior to RNA sequencing (RNA-seq) samples were processed (mRNA purification and fragmentation, cDNA synthesis, end repair, 3' adenylation, adaptor ligation, and DNA enrichment) using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) and AMPure XP beads (Beckman Coulter, Brea, CA) per the manufacturer's instructions. DNA fragment size was determined using Experion DNA 1K chips (Bio-Rad, Hercules, CA) and library quantification was completed using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA). Raw data in FASTQ format was processed for quality using CLC Bio Genomic Workbench (Qiagen, Valencia, CA). The transcriptome was assembled using the annotated porcine translational research database (version NR 112918)  as a reference genome