Acute Transcriptomic Response After Mouse Spinal Cord Injury

In order to characterize genomic response and identify molecular marker for acute neural injury, we performed RNA-sequencing 4 hours after spinal cord injury. We found a group of genes with significant differential expression (DEG) after Benjamini-Hochberg FDR multiple corrections. These DEGs mainly include early response genes, neuroinflammation, and cell injury and death. Notely, activating transcription factor 3 (ATF3) is one of the most significantly upregulated genes by 9.9 folds and is a well-recognized molecular marker for DRG sensory neuron injury in peripheral nerve injury model. Unilateral C5 (cervical) contusion injury or laminectomy only was performed in wildtype mice (n=3 in each group). Spinal cord tissue was collected 4 hours after SCI and stored at -80 degrees. Total cellular RNA was prepared using TRIzol and RNA miniprep kit (Qiagen). RNA sequencing was performed using 1ug total RNA. Sequencing type: single-end 50bp by Illumina HiSeq 4000, Lexogen Quantseq Forward library kit with STAR_2.7.2b aligner. mm10, Ensembl mouse GRCm38.96 Alignment Genome was used.