Difference between revisions of "Overview"

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Revision as of 14:25, 27 January 2013

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

Maintaining the axolotls

Feeding

Artemia (Brine shrimp eggs)

Brine shrimp eggs are metabolically inactive and can remain in total stasis for two years while in dry oxygen-free conditions, even at temperatures below freezing. This characteristic is called cryptobiosis meaning "hidden life" (also called diapause). While in cryptobiosis, brine shrimp eggs can survive temperatures of liquid air (−190 °C or −310.0 °F) and a small percentage can survive above boiling temperature (105 °C or 221 °F) for up to two hours.

Once placed in brine (salt) water, the cyst-like eggs hatch within a few hours. The nauplii, or larvae, are less than 0.5 mm in length when they first hatch. Brine shrimp have a biological life cycle of one year, during which they grow to a mature length of around one centimeter on average. This short life span, along with other characteristics such as their ability to remain dormant for long periods, has made them invaluable in scientific research, including space experiments. This ability has also enabled the use of a hybrid of brine shrimp, bred to grow larger and live longer, as Sea-Monkeys.

Artemia Hatching Preparation: Protocol for 15 Ltr.

Switch on the bubbler.
Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already.
Switch on the heating. And make sure that the light on the top is on ☺ Add 50-60 ml full of dried artemia (Stored at 40C) to this.

Hatching preparation
  • The following protocol is considered for 15 l solution.
  • Switch on the bubbler.
  • Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already.
  • Switch on the heating. And make sure that the light on the top is on.
  • Add 50-60 ml full of dried artemia (Stored at 40C) to this.

Keep it like this for 2 days with aeration. And >200 Lux of light.
Usually they hatch within few hours but It is good to keep for 2 days to achieve a good hatching.
During these two days temperature can be 18°-20°C.
Make sure hatching container is not getting clogged during these two days.

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

  • Limb bud expression

Germ-line transmitted
PM33 Col1A2-TFP-NLS-T2A-mERt-Cre-ERt Sce1 Prayag Murawala Bone and fibroblast

  • Bone expression

  • 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 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/axolotl/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.gz Dunja Knapp
Amputated limb (36h) Amputated axolotl forelimb (36hpa) Limb Single-ended 76bp 65,250,768 FastQ Limb/36h_amp.fastq.gz Dunja Knapp
Amputated limb (72h) Amputated axolotl forelimb (72hpa) Limb Single-ended 76bp 62,970,898 FastQ Limb/72h_amp.fastq.gz Dunja Knapp
Lateral wound (36h) Injured (lateral wound) axolotl forelimb (36hpw) Limb Single-ended 76bp 66,361,470 FastQ Limb/36h_lw.fastq.gz Dunja Knapp
Lateral wound (72h) Injured (lateral wound) axolotl forelimb (72hpw) Limb Single-ended 76bp 64,133,834 FastQ Limb/72h_lw.fastq.gz Dunja Knapp
Sanger

The data can be found under //biodata/groups/crtd_tanaka/axolotl/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/axolotl/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/axolotl/Microarrays. Please, also consult the file Contents.txt in the experiment directory for more details.

Name Description Timepoints Tissue Location Author Raw data (*.tiff) present Remarks
Fin vs bulk Timecourse microarray experiment using fin and bulk tissue 0, 1d, 3d Mature tail: fin and bulk Fin_vs_bulk Eugeniu Nacu Yes
Limb Timecourse microarray experiment using limb 0, 3h, 6h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h Mature limb Limb_timecourse Eugeniu Nacu Yes
Tail timecourse Timecourse microarray experiment using tail 0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h Mature tail Tail_timecourse Eugeniu Nacu Yes
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 Limb_timecourse_2 Dunja Knapp No
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