Figure 1.

Regeneration-associated genes display stage-specific expression after optic nerve injury. (A) Schematic depicting stages of optic nerve regeneration from 0–12 days post-injury (dpi). (B) RNA-seq results generated from dissected retinas of adult zebrafish at 7–9 months of age. Transcripts from retinas dissected 2–12 days post optic nerve crush were compared with those from uninjured animals. Together, 7,480 transcripts were expressed at either higher (red = upregulated) or lower (blue = downregulated) levels in injured retina at 2, 4, 7, and/or 12 dpi when compared to control retinas (0 dpi), adjusted p values < 0.05. (C) Temporally clustered transcripts demonstrate stage-specific enrichment of canonical pathways. Expression heatmaps produced from Z-scores (calculated using transcripts per million [TPM] estimates) of 4,614 differentially-expressed transcripts with adjusted p values < 0.01. Mean normalized transcript counts were generated for each transcript across all samples at all time points. Each row represents a single transcript where each biological sample was compared to the mean, with red and blue indicating standard deviation above and below the mean, respectively. Each column represents one of the three biological replicates for each time point. Genes within each cluster were analyzed by Ingenuity Pathway Analysis (IPA) using –log(p-value) > 4, to identify pathways expressed in a regeneration stage-specific manner. NA, not applicable, indicates that no pathways were detected that met our significance threshold.