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Notes.org

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+#+TITLE: Notes
+* Methods
+** Whole genome sequencing -> PacBio, along with Illumina for error correction in 1% of contig bases
+** Development of a new genome assembler, due to the large genome size (x10 human size) -> MARVEL
+** Verification of the genome assembly using non-exonic ultraconserved elements (UCEs) and generation of a gene catalogue using mRNA to determine if these coded for conserved eukaryotic genes
+** Previously developed molecular toolkit -> germline transgenesis, CRISPR gene mutation, viral transfection... -> Identification of the regeneration cells
+* Findings
+** The median intron size is quite large (12-17 times compared to humans) -> Smaller intron sizes in non-developmental genes, which could facilitate rapid transcription and upregulation
+- Pax family of genes:
+
+ | Presence | Absence |
+ | Pax10    | Pax7    |
+ |          | Pax3    |
+
+Pax3 and its cis-regulatory elements seem to be absent due to a deletion, although experiments performed using CRISPR mutate the gene show that Pax7 performs the functions of Pax3 along with the usual Pax7 functions in axolotl
+
+** Limb regeneration
+*** Use of published mRNA and miRNA transcripts and the authors' own transcriptional profiling -> identification of 5 upregulated transcripts
+| Protein             | Function              |
+| similar to tectorin | Extracellular matrix  |
+| Ly6                 | uPAR surface receptor |
+*** Mapping non-coding RNAs -> 93 pre-miRNA, 42 novel miRNAs
+* Future work
+Model organism to study the evolutionary basis of its regeneration ability