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

Lab duties


Protocols


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.

Transgenic lines

Axolotl (A.mexicanum)

Name Construct Method of transgenesis Author Tissue Image(s) Remarks
PM28 Prrx1-TFP-NLS-T2A-mERt-Cre-ERt Sce1 Prayag Murawala Limb bud and limb blastema
  • Error creating thumbnail: File missing

    Limb bud expression

Germ-line transmitted
PM33 Col1A2-TFP-NLS-T2A-mERt-Cre-ERt Sce1 Prayag Murawala Bone and fibroblast
  • Error creating thumbnail: File missing

    Bone expression

  • Error creating thumbnail: File missing

    Bone expression in limb bud

Germ-line transmitted

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
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