Objectives To determine if RNA collected from pancreatic tissue, without the use of RNAlater, is useful for RNA sequencing (RNA-seq) despite degradation, and if so, then, via RNA-seq analysis, how does gene expression vary between pancreatitis etiologies. Methods Data were assessed in 2 dimensions, based on RNA-seq signal shape assessed by RSeQC v.2.6.4 and RNA expression after accounting for different degrees of degradation. Results Six measures of RNA characteristics (median RNA fragment size, reads per million kilobases saturation, transcript integrity number, distribution of hexamers, percentage of nucleotides that are guanine or cytosine, and duplicated reads) were significantly different between hereditary pancreatitis and idiopathic pancreatitis. Differential expression analysis revealed that 150 genes were differentially expressed between hereditary and idiopathic etiologies, 197 genes were differentially expressed between alcoholic and idiopathic etiologies, and 200 genes were differentially expressed between alcoholic and hereditary etiologies. We then determined that many enriched pathways between hereditary and idiopathic etiologies are related to the matrisome, and many of the enriched pathways between alcoholic and idiopathic etiology or hereditary etiology are related to ion transport. Conclusions We found distinct RNA-seq signals between different pancreatitis etiologies in both of the dimensions in critical pathways for pancreas biology.
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- RNA quality
- differential expression
- pathway enrichment