Search

Additional file 6. A summary list of all DESR genes, sorted by primary functional category and time point of differential expression, along with relevant references supporting the functional assignment. Note that genes were assigned their human gene ortholog symbols, without reference to whether they were L or S homeologs, or paralogs.

Additional file 3. Temporal patterns of gene expression and shared injury-response genes between regenerative vs. non-regenerative tissues, as determined by DESeq2. A) Regenerative tissues [i.e., SCI tadpole hindbrain (SCI Tadpole) and ONC juvenile frog eye (ONC Juvenile)] shared similar temporal patterns of numbers of significant (FDR

Additional file 5. Scatterplot representation of the Principal Component Analyses (PCA) of gene expression profiles. Ellipses group biological replicates for each indicated condition (experimentals, solid squares; controls, empty squares), indicating variation among samples. A-C, PCA of tadpole and juvenile hindbrain after spinal cord injury (SCI), and of juvenile frog after optic nerve crush (ONC), respectively. In C, expression profiles from the operated eye were compared with those of the contralateral, unoperated eyes within the same animals. D, PCA of all 17 conditions combined, supporting the tissue-specific nature of gene expression profiles. Conditions were the same as in A-C, except that data from eyes of animals receiving no injury was included (open triangles, Frog Eye, Unop). E, PCA of tadpole and juvenile frog hindbrain samples after spinal cord injury, supporting the conclusion that the differences in gene expression profiles between the time points at which numbers of differentially expressed genes reached their peaks (3 days in juvenile frog hindbrain and 1 week in tadpole hindbrain) were more than just a kinetic difference in the timing of expression of the same differentially expressed genes. Abbreviations: ONC, optic nerve crush; PC1, principal component axis 1; PC2, Principal Component axis 2; SCI, spinal cord injured; TX, spinal cord transected; Unop ONC - unoperated eye, contralateral to the operated eye; Frog Eye, Unop - eyes from unoperated animals; wk., week.