A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors

Discovery of genes driving axolotl limb regeneration has been challenging due to limited genomic resources. We assembled 42 RNA-Seq samples totaling approximately 1.3 billion 100 base paired-end reads using Trinity (Grabherr M.G. et al, Nature Biotechnology, 2011; Haas B.J. et al, Nature Protocols, 2013): https://github.com/trinityrnaseq/trinityrnaseq/wiki). We created a transcriptome with complete sequence information for most axolotl genes, identified transcriptional profiles that distinguish blastemas from differentiated limb tissues, and uncovered functional roles for cirbp and kazald1 in limb regeneration. To identify transcripts that are essential for regeneration and to provide a resource for axolotl researchers we profiled 42 samples across 16 tissues, from distinct locations among intact and regenerating limbs, relevant cell types, and other progenitor-rich samples using RNA-sequencing. The SRA study accession for these data is: SRP065567. The BioProject accession is: PRJNA300706. The TSA accession for the transcripome assembly is: GFBM000000000.