Getting More out of RNA-Seq Data: Transcriptomic Analysis of Ischemic Stroke

Abstract
In recent years, RNA sequencing has become a standard method for genome-wide transcriptional analysis. Despite the extensive informational content of RNA-Seq data, many studies limit their scope to differentially expressed genes and/or pathway enrichment analysis, leaving substantial part of information unexplored. Here, we present a comprehensive transcriptomic analysis of the ischemic stroke in young and aged animals. We assessed differential gene expression across injury status and age, performed detailed pathway analysis and unsupervised co-expression analysis, identifying modules of genes associated with the various response to injury. We complemented these results with estimation of cell-type proportion changes using computational deconvolution techniques and assayed our results with findings from previous studies of similar design and publicly available databases. By employing these simple, yet often underutilized analytical approaches we found disease signatures consistent with literature and extend these results with new findings. We show strikingly variable response of different cell types and specific cellular pathways between young and aged ischemic animals, particularly related to immune response. Together, these results paint a picture of ischemic stroke as a complex age-related disease and provide insights into interaction of age and stroke on cellular and molecular level.