Overview

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Introduction

On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.

Axolotl

Maintainance

In this section you will find some general information on how to maintain the animals.

Feeding

This section will give you an overview of how to feed the axolotls.

Interesting observations

In the following section you can find some interesting observations concerning the axolotl, its behavior, caveats of the transgenics and many more.

Lab duties


Protocols

    Cell culture

  • Blastema cells
  • Baculovirus titration
  • Myoblasts electroporation
  • Adhesive cell culture
  • Electroporation of blastema cells
  • Electroporation of neural epithelia cells (axolotl spinal cord)
  • mESC culture/Cyst formation
  • Neurosphere culture

    • Histology

  • Double Immunostaining via antigen retrieval (Sherry)

    • Antibody

  • labeled AB staining

    • Molecular biology

  • Metamorphosis protocol (Sherry)
  • DNA Digestion (Plasmid)
  • RNA Extraction (axolotl tissue)
  • RNA formaldehyde gels

    • Lab business

    Ordering database

    Use the following ordering database to place your orders.

    Booking calendars

    Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.

    Genetics

    Transgenic lines

    Markers

    Marker Full name Target Remarks Link
    DAPI/Hoechst 4',6-diamidino-2-phenylindole Nuclei Incorporates into the DNA DAPI, Hoechst
    PCNA Proliferating-Cell-Nuclear-Antigen Dividing cells PCNA
    SOX2 SRY (sex determining region Y)-box 2 Preferentially neuronal lineage Progenitor marker for both spinal cord and brain SOX2
    PAX6 Paired box protein Pax-6 Brain/spinal cord aka aniridia type II protein (AN2) or oculorhombin PAX6
    PAX7 Paired box protein Pax-7 Satellite cells/spinal cord/brain PAX7
    MHC Myosin heavy chain Muscle fibers MHC
    MYF5 Myogenic factor 5 Myoblasts Regulates muscle differentiation, labels cycling myoblasts MYF5
    TUBB3 ßIII-tubulin Axons TUBB3
    MBP Myelin basic protein Schwann cells
    PRRX1 Paired mesoderm homeobox protein 1 Connective tissue progenitors in Limb bud and Limb Blastema PRRX1
    SMA Smooth muscle actin Blood vessels/endothelial cells
    GFAP Glial fibrillary acidic protein Glia GFAP
    NeuN Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3 Differentiated nerve NeuN
    LEU7/HNK1/B3GAT1/CD57 Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 Schwann cells B3GAT1
    XBRA Xbrachyury Mesoderm during gastrula stage Brachyury
    MSX1 Muscle segment homeobox, Msh homeobox 1 Undifferentiated cells Transcriptional repressor during embryogenesis MSX1
    Trypan blue Dead tissues or cells Vital stain Trypan blue
    MEF2C Myocyte-specific enhancer factor 2C Differentiated muscle cells aka MADS box transcription enhancer factor 2, polypeptide C MEF2C
    PH3 Phospho-Histone H3 Mitotic cells
    BrdU Bromodeoxyuridine Cells in S-phase BrdU
    CASP3 Caspase 3 Dying cells CASP3
    GDF5 Growth/differentiation factor 5 Joints Joint development marker GDF5
    Survivin Cleavage furrow aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5 Survivin
    MAP2 Microtubule-associated protein 2 Neurons MAP2
    SOX9 SRY (sex determining region Y)-box 2 Cartillage progenitors SOX9
    MBP Myelin basic protein Myelin sheath MBP

    Digital data

    Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. Select a category from the list below in order to view or download the data.

    Fileservers

    Location Volume size Description Access Location (console only)
    //biodata/groups/crtd_tanaka 16 TB General purpose storage space Entire Tanaka lab biocluster: /group/crtd_tanaka
    //biodata/groups/tanaka-ests 247 GB EST sequences Entire Tanaka lab biocluster: /group/tanaka-ests
    //biodata/groups/axolotl-transcriptome 500 GB Axolotl transcriptome data Elly, Sergej biocluster: /projects/axolotl-transcriptome
    //biodata/groups/tanaka-saori 878 GB Special directory for Saori's data Elly, Saori, Sergej biocluster: /group/tanaka-saori
    Error creating thumbnail: File missing
    NOTE: The path is different, when accessing the file server from the console.

    Literature

    Databases

    • Axolotl transcriptome website contains the Axolotl transcriptome assemblies
    • Newt transcriptome website contains the Newt transcriptome assembly
    • Red spotted newt transcriptome website contains the red spotted newt transcriptome assembly
    • Axolotl EST database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.
    • Short insert cDNA library
    • CURRENTLY UNAVAILABLE! Axologle database contains expression profiling data of Axolotl limb regeneration
    • CURRENTLY UNAVAILABLE! Axolotl BLAST database contains several different BLAST-able Axolotl transciptome assemblies

    Datasets

    Interesting links

    Lab life

    • Lab photos
    • Further pictures can be found in /biodata/groups/crtd_tanaka/LabFun/
    • The recepies for Heino's farewell present can be found under /biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/
    • The video of the visit of the EU commissioner can be found under /biodata/groups/crtd_tanaka/LabFun/
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