At the 30 d post-SCI endpoint, a 9 mm segment of spinal cord centered on the site of injury was collected and subdivided into three 3 mm segments that encompassed the injury epicenter, or the 3 mm of adjacent tissue rostral (“Above”), or caudal (“Below”). 3 mm spans were chosen as this length essentially encompasses the injury epicenter by visual inspection. For the uninjured controls, the full 9 mm section of spinal cord corresponding to the identical anatomical levels as the SCI group (T11 – S1) was collected and processed collectively. Total RNA was prepared using RNA Stat60 (Tel-Test, Friendswood, TX) following the manufacturer's instructions. RNA libraries were prepared using 200 ng of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).