RNA-sequencing of regenerating planaria Dugesia japonica

We employed RNA-sequencing with surgically resected planaria and cysteinyl-specialized pro-resolving mediators (cys-SPMs), including MCTR3, PCTR3 and RCTR3 to identify genes and pathways activated by cys-SPMs. Overall design: Planaria (Dugesia japonica; Dj) were kept in water (Poland Spring) at 20°C and starved for 7 days before surgery. Briefly, head resection was performed (post-ocular surgical injury), and posterior portions were then placed in water together with MCTR3, PCTR3, RCTR3 (10 nM) or vehicle (0.1% ethanol v/v in water). Forty-eight hours later, planaria were collected, RNA isolated and submitted to Molecular Biology Core Facilities at Dana-Farber Cancer Institute (Boston, MA) for paired-end RNA sequencing using an Illumina NextSeq 500 sequencing system. Bioinformatics was carried out using Dj transcript sequences with the Bioinformatics and Biostatistics Core at Joslin Diabetes Center (Boston, MA).