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
• Feeding

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

Molecular biology

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
  • Electroporator
  • 2nd electroporator
  • Microinjector
  • Stereoscope
• Confocal microscopes
  • Leica LSM
• Cryostats
  • Cryostat 1
  • Cryostat 2
• Microtome
  • Microtome

Transgenic lines

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

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.

Literature

Theses

Title	Summary	Author
Reconstitution of three-dimensional neuroepithelia from mouse and human pluripotent stem cells		Yu Zhu

Publications

Title	Summary	First author	Year	Journal

Databases

• 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 several different Axolotl transciptome assemblies

Datasets

Sequences

Illumina

The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina.

Name	Description	Tissue	Type	Read length	Reads	Format	Location	Author	Remarks
Mature spinal cord	Mature axolotl spinal cord	Spinal cord	Paired-ended	100bp	65,753,941	FastQ	SpinalCord/mSC.fastq.tar.gz	Akira Tazaki
Injured spinal cord	Injured axolotl spinal cord, 6dpi	Spinal cord	Paired-ended	100bp	78,459,950	FastQ	SpinalCord/6diSC.fastq.tar.gz	Akira Tazaki
Mature spinal cord	Mature axolotl spinal cord, replicate 2, crossing 142x5	Spinal cord	Paired-ended	100bp	101,769,559	FastQ	SpinalCord/mSC_142x5.fastq.tar.gz	Akira Tazaki	Due to a sequencer failure only the first 66 bases are safe
Mature spinal cord	Mature axolotl spinal cord, replicate 3, crossing 96x6	Spinal cord	Paired-ended	100bp	95,946,545	FastQ	SpinalCord/mSC_96x6.fastq.tar.gz	Akira Tazaki	Due to a sequencer failure only the first 66 bases are safe
Injured spinal cord	Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5	Spinal cord	Paired-ended	100bp	96,626,387	FastQ	SpinalCord/6diSC_142x5.fastq.tar.gz	Akira Tazaki	Due to a sequencer failure only the first 66 bases are safe
Injured spinal cord	Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5	Spinal cord	Paired-ended	100bp	99,855,603	FastQ	SpinalCord/6diSC_96x5.fastq.tar.gz	Akira Tazaki	Due to a sequencer failure only the first 66 bases are safe
Mature limb	Mature axolotl forelimb	Limb	Single-ended	76bp	65,934,228	FastQ	Limb/Mature.fastq.tar.gz	Dunja Knapp
Amputated limb (36h)	Amputated axolotl forelimb (36hpa)	Limb	Single-ended	76bp	65,250,768	FastQ	Limb/36h_amp.fastq.tar.gz	Dunja Knapp
Amputated limb (72h)	Amputated axolotl forelimb (72hpa)	Limb	Single-ended	76bp	62,970,898	FastQ	Limb/72h_amp.fastq.tar.gz	Dunja Knapp
Lateral wound (36h)	Injured (lateral wound) axolotl forelimb (36hpw)	Limb	Single-ended	76bp	66,361,470	FastQ	Limb/36h_lw.fastq.tar.gz	Dunja Knapp
Lateral wound (72h)	Injured (lateral wound) axolotl forelimb (72hpw)	Limb	Single-ended	76bp	64,133,834	FastQ	Limb/72h_lw.fastq.tar.gz	Dunja Knapp

Sanger

The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger.

Name	Description	Tissue	Sequences	Location	Author	Remarks
LimbBlastema	Limb blastema library	Limb blastema	20160 (RSD) / 15648 (SCF)	SCF files: LimbBlastema/LB_SCF.gz RSD files: LimbBlastema/LB_RSD.gz	Akira Tazaki
NeuraTube	Neural tube library	Teural tube	4896 (RSD) / 7905 (SCF)	SCF files: NeuralTube/NT_SCF.gz RSD files: NeuralTube/NT_RSD.gz	Akira Tazaki

Roche/454

The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/454.

Name	Description	Tissue	Reads	Format	Location	Author	Remarks
454	Mixed 454	Mixed	1,208,954	Fasta/Qual	Ax_454.tar.gz	n/a

Microarrays

The data can be found under //biodata/groups/crtd_tanaka/LabData/Microarrays. Also consult the file Contents.txt in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory Raw in the experiment directory.

Name	Description	Timepoints	Tissue	Array type	Location	Author	Remarks
Fin vs bulk	Timecourse microarray experiment using fin and bulk tissue	0, 1d, 3d	Mature tail: fin and bulk	Agilent, 44000	Fin_vs_bulk	Eugeniu Nacu
Limb	Timecourse microarray experiment using limb	0, 3h, 6h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h	Mature limb	Agilent, 44000	Limb_timecourse	Eugeniu Nacu
Tail timecourse	Timecourse microarray experiment using tail	0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h	Mature tail	Agilent, 44000	Tail_timecourse	Eugeniu Nacu
Limb timecourse 2	Timecourse microarray experiment using limb	0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h	Mature limb and limb bud	Agilent, 44000	Limb_timecourse_2	Dunja Knapp