Next Generation Sequencing of zebrafish spinal cord transcriptomes before and after injury

The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish spinal cord before and after injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one, two, four, and six weeks post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries (N=4-5) were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40-80 million sequence reads per sample to the zebrafish genome and identified 37,603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before and after injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue, the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one, two, four, and six weeks post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent (Invitrogen), and cDNA libraries (N=4-5) were subjected to Illumina sequencing according to the manufacturer's protocol.