Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons
Expression profiling by high throughput sequencing
Summary
Xenopus is uniquely suited for addressing the question of whether a core gene expression program for successful CNS axon regeneration exists, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed RNA-Seq after optic nerve and spinal cord injury to identify trauma-induced genes shared between two regenerative CNS regions, but not shared with a non-regenerative one. We provide these data as a resource for new avenues of investigation into the molecular basis of tissue regeneration.
Overall design
RNA-seq (30 million nominal reads per sample) was performed on 51 samples: operated juvenile frog eye and contralateral unoperated eye after optic nerve injury at three different timepoints (3 days, 11 days, 3 weeks), plus surgiically naïve frog eyes, with 6 pooled eyes for each sample; tadpole hindbrain after spinal cord transection plus age-matched unoperated controls at three timepoints (3 days, 7 days, 3 weeks), with 5 pooled hindbrains for each sample; juvenile frog hindbrain after spinal cord transection at 3 timepoints (3 days, 7 days, 3 weeks), plus unoperated hindbrain control, with 5 pooled hindbrains for each sample.
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