Mucosal transcriptome of rectal biopsies in treatment-naïve, pediatric ulcerative colitits patients

Using recal mucosal biopsies, collected prior to treatment in new-onset pediatric ulcerative colitis patients, we performed RNAsequencing to generate transcriptomic profiles linked to pathogenesis, severity, and treatment response. Biopsies were obtained from 206 new-onset patients during diagnostic colonoscopy, using the Qiagen AllPrep RNA/DNA MiniKit. PolyA-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, TruSeq RNA sample library preparation (Illumina, San Diego, CA), and paired-end 75bp sequencing was performed. Reads were quantified by kallisto [32], using Gencode v24 as the reference genome and Transcripts per Million (TPM) as an output. We included 14,085 protein-coding mRNA genes with TPM above 1 in 20% of the samples in our downstream analysis.