The Amex_PQ.v4 chromosomal scale assembly reported by Smith et al 2019 can be accessed using the UCSC Genome Browser

  

Variant and SNP density track session from Timoshevskaya et al 2020: 

Timoshevskaya N, Voss SR, Labianca CN, High CR, Smith JJ. 2020. Large-scale variation in SNP density within the laboratory axolotl (Ambystoma mexicanum). Developmental Dynamics, In Press.

 

EMBARGO/FAIR USE OF EPIGENETICS DATA: We are delighted to release unpublished epigenetics tracks to the community. We encourage others to use these data, but in doing so we also expect that they will respect our right to first presentation (including journal publications, pre-prints such as in bioRxiv, public conference talks, and press releases) of a genome-wide analysis of these tracks. This includes the use of genome-wide epigenetics data for generalized descriptions of gene-regulatory patterns in axolotl and evolutionary/developmental/regeneration analyses, on behalf of ourselves as data producers and collaborators. Therefore, please respect the embargo on the presentation of analyses using pre-publication data that we release via this website and relevant archives. Similar fair use statements apply to many genome assemblies such as those released by the Sanger Institute and the VGP.

Exceptions to the policy are for analyses of either a single locus, or a single gene family, or for use as a reference for mapping reads from independent studies. Individual tracks and datasets will be considered released from this embargo when they are expressly published, and the relevant reference(s) will be added to this website at that time. For any queries about using the data, referencing/publishing analyses based on pre-publication data or interest in contributing to genome-scale analyses please contact This email address is being protected from spambots. You need JavaScript enabled to view it..  We are also happy to make tracks from other groups available under this same fair use policy.

Chemical Screening

Axolotls can be used to efficiently screen chemicals for toxicity and effects on tissue regeneration. This database reports chemicals that were screened using an axolotl embryo tail regeneration model. Chemical outcomes on tail regeneration were classified as either inhibitory, non-inhibitory, or toxic, and chemicals that were validated in a second screen are noted. The database can be searched using a chemical's name, structure (SMILES), molecular weight (ML), or bioactivity.

To learn how to perform the axolotl embryo tail regeneration assay, see the 2020 Axolotl Newsletter. 

 

Search for Chemical Name/SMILES/MW/Bioactivity                                                                                                                                                                                                                                                                           

     
 

Example Query:

Chemical Name = Romidepsin 

SMILES = C\C=C1\NC(=O)[C@H]2CSSCC\C=C\[C@H](CC(=O)N[C@@H](C(C)C)C(=O)N2)OC(=O)[C@@H](NC1=O)C(C)C     

MW = 540.69

Bioactivity = Histone deacetylase inhibitor (HDAC)

Outcome = Inhibits tail regeneration at 10 uM

Validated = Yes


We provide three assemblies for BLAST search of the A. mexicanum genome. To get search results faster, limit the number of sequences in your query.

1. The Amex_PQ.v4 database was built from a chromosomal scale assembly reported by Smith et al 2019. For small chromosomes, the results of BLAST searches are reported for the entire chromosome. For large chromosomes, the results of BLAST searches are reported for P or Q chromosome arms, or regions within P or Q chromosome arms.

For example, Chr1P is split into Chr1P:0-1,000,000,000 and Chr1P:1,000,000,000-1,477,091,900. In this case, alignments are reported relative to the position 0 or 1,000,000,000. A Chr1P alignment spanning 4,500 - 5,300 will be reported as either Chr1P:4500-5300 or Chr1P:1,000,004,500-1,000,005,300.

 
2. The ambMex3 database was built from an assembly published by Nowoshilow et al 2018.
 

3. The Amex_female.v1 database was built from an assembly used by Keinath et al 2018 to identify the sex-determining region in the axolotl genome.