GSM2536335: LIB98726_SAM24318646: uncrushed dlki; Mus musculus; RNA-Seq
RNA-seq was performed from a separate cohort of animals to compare gene expression changes in eye retina three days post acute injury (optic nerve crush) from mice treated with vehicle (MCT, n=5) or with (n=5) the DLK inhibitor GNE-3511 (75mg/kg dosed 60 and 68 hr post-injury). A total of four experimental groups were included as follows: vehicle-treated 1) uncrushed retina, 2) vehicle-treated crushed retina, 3) GNE-3511-treated uncrushed retina, and 4) GNE-3511-treated crushed retina. Total RNA was extracted using Qiagen RNeasy kit as per manufacturerâs protocol including the on-column DNase digestion. Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies). 0.5 Âµg of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Size of the libraries was confirmed using Fragment Analyzer (Advanced Analytical Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads.