#+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