Overview

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

Chemicals

• Antibiotics
• Benzocaine
• Fibronectin
• Gelatine
• Liquid nitrogen
• Primary antibodies
• Secondary antibodies
• Serum immunostaining

Hardware

• Autoclave
• Cryostat
• Dissecting microscopes
• Leica confocal microscope
• Vacuum pumps
• Waterbath

General

• Ordering common stuff
• Heat-shock competent cells

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)

Molecular biology

• Metamorphosis protocol (Sherry)

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.

• Fluorescence microscopes
  • Olympus SZX 16
  • New Olympus SZX 16
  • Olympus OVK
  • Axio Observer
• Microinjectors and electroporators and dissecting microscope
  • Room 0.232
    • Nepa Gene
    • ECM 830
    • Olympus dissecting microscope
  • Lab
    • Olympus (next to the axolotls)
    • Olympus (next to the Microtome)
• Confocal microscopes
  • Leica LSM
• Cryostats
  • Cryostat 1
  • Cryostat 2
• Microtome
  • Microtome
• Paraffin embedding station
  • Paraffin embedding station

Genetics

Transgenic lines

• Axolotl (A.mexicanum)
• Frog (X.laevis)

Markers

Marker	Full name	Target	Remarks
DAPI/Hoechst		Nuclei	Incorporates into the DNA
PCNA	Proliferating-Cell-Nuclear-Antigen	Dividing cells
Sox2		Preferentially neuronal lineage	Progenitor marker for both spinal cord and brain
PAX6		Brain/spinal cord
PAX7		Satellite cells/spinal cord/brain
MHC	Myosin heavy chain	Muscle fibers
Myf5		Muscle fibers	Labels cycling myoblasts
ßIII-tubulin		Axons
MBP	Myelin basic protein	Schwann cells
Prrx1		Blastema/mesodermal cells of limb bud
SMA		Blood vessels/endothelial cells
GFAP	Glial fibrillary acidic protein	Glia
NeuN		Differentiated nerve
Leu7		Schwann cells
Xbra	Xbrachyury	Mesoderm during gastrula stage
Msx1		Undifferentiated cells	Transcriptional repressor during embryogenesis
Trypan blue		Dead tissues or cells	Vital stain
Mef2c		Differentiated muscle cells
PH3		Mitotic cells
BrdU		Cells in S-phase
Casp3		Dying cells
Gdf5		Joints	Joint development marker
Survivin		Cleavage furrow
MAP2
SOX9		Cartillage progenitors

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

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NOTE: The path is different, when accessing the file server from the console.

Literature

• Theses
• Publications

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.
• Axologle database contains expression profiling data of Axolotl limb regeneration
• Axolotl BLAST database contains several different BLAST-able Axolotl transciptome assemblies

Datasets

• Sequences
  • Illumina
  • Sanger
  • Roche/454
• Microarrays

Interesting links

• Visible in the invisible: a movie introducing a new image processing ana analysis technique developed at the MIT.

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/