Transcriptome of Subcortical White Matter and Spinal Cord After Spinal Injury and Cortical Stimulation

Spinal cord injury disrupts ascending and descending neural signals causing sensory and motor dysfunction below the injury. Neuromodulation with electrical stimulation is used in both clinical and research settings to induce neural plasticity and improve functional recovery following injury. However, the mechanisms by which electrical stimulation affects recovery remain unclear. In this study we examined the effects of cortical electrical stimulation following injury on transcription at several levels of the central nervous system. We performed a unilateral cervical spinal contusion injury in rats and delivered stimulation for one week to the contralesional motor cortex to activate a descending motor tract.RNA was purified from bilateral subcortical white matter, and 3 levels of the spinal cord. Here we provide the complete data set in the hope that it will be useful for researchers studying electrical stimulation as a therapy to improve recovery from the deficits associated with spinal cord injury. Overall design: Four adult female Long-Evans rats weighing 275-350 grams sustained a cervical level 4 (C4) hemi-contusion injury, resulting in forelimb functional deficits. Electrodes were implanted into the caudal forelimb areas of the contralateral motor cortex. Two animals received stimulation for one week at a current 80% of that required to evoke movement in the affected forelimb. Control animals were injured and implanted without stimulation. At the end of the experiment spinal cords and brains were removed, and five subregions were snap frozen in liquid nitrogen for sequencing. Region 1 was an approximately 5 mm3 block of subcortical white matter (without cortex) directly below the implantation/stimulation site. Region 2 was the same region on the contralateral side. Region 3 was spinal cord rostral to the injury (~C2-C4). Region 4 was the lesion epicenter (C4). Region 5 was the spinal cord caudal to the injury (~C5-C7). The spinal cord regions included both gray and white matter, neuron cell bodies and processes and glia. Complete RNA was isolated and sequenced and the reads were aligned to a rat reference genome.