Evaluation of Multiple Differential Gene Expression Pipelines to Study Spinal Cord Injury in Monodelphis domestica

Injury to the mature spinal cord typically results in complete loss of function below the level of the injury. This loss of function is usually permanent and currently there are no effective curative treatments. However, when the spinal cord is injured during early development the axons have the capacity to grow across the injury site and form functional circuitry. This ability is lost as the as the spinal cord matures.

In this study, we employ a developmental model of spinal injury using Monodelphis domestica, a grey short tailed opossum, whose young are born at an extremely immature stage of development (equiv. to rodent embryonic day E13). In these animals, spinal injury in 7-day-old pups (P7) results in pronounced axonal regrowth through the injury site, but following injuries made 28-days (P28) no regrowth occurs.

Here we present RNA sequencing analyses aimed at identifying key developmentally regulated facets of the nervous system’s response to injury that result in a state that is either ‘permissive’ or ‘non-permissive’ to axonal regrowth.

In this study, we have evaluated multiple pipelines for differential gene expression analysis. This sort of comparative study will enable us to obtain a more optimum gene set which will in turn help better address the biological questions at hand. Workflows described in this study integrate a variety of tools for alignments, read count generation, differential gene expression and pathway analysis. A full understanding of these genetic factors may yield new therapeutic targets in future.