GEO DataSets

(Submitter supplied) Treatment with midkine inhibitor iMDK inhibits limb regeneration. To elucidate the transcriptional mechanisms of iMDK treatment, we sequenced regenerating limbs treated with either DMSO or iMDK (bulk) in biological triplicate at 11 days post-amputation (dpa).

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24679

6 Samples

Download data: MATRIX

(Submitter supplied) The wound epidermis is required for limb regeneration. To elucidate the roles of the wound epidermis during early regeneration, we examined how the transcriptional programs of early dividing cells (enriched for blastemal progenitors) and non-dividing cells in regenerating stump tissues as well as epithelial cells change when we prevented wound epidermis formation.

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22800

9 Samples

Download data: MATRIX

(Submitter supplied) Regeneration of complex multi-tissue structures, such as limbs, requires the coordinated effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema have been extensively studied via histology, grafting, and bulk-tissue RNA-sequencing. However, studying the contributions of these tissues is hindered due to limited information regarding the molecular identity of the cell types in regenerating limbs. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24679

3 Samples

Download data: FASTA, TXT

(Submitter supplied) The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. more...

Organism:

Mus musculus; Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14997 GPL11002

20 Samples

Download data: TXT

(Submitter supplied) Blastema formation is a hallmark of limb regeneration that requires proliferation and migration of progenitors derived from many tissues to the amputation plane. To better understand the genetic programs that initiate limb regeneration, we reasoned that blastemal progenitors would be among early proliferating cells in the stump following amputation. Here we separately profiled dividing and non-dividing stump tissues, as well as the wound epidermis, during early axolotl limb regeneration to examine transcriptional programs of blastemal progenitors. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22800

27 Samples

Download data: CSV, TAB, XLSX

(Submitter supplied) Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18413 GPL14875

12 Samples

Download data: TXT

(Submitter supplied) Previous studies of vertebrate appendage regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. more...

Organism:

Polypterus senegalus

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21070

8 Samples

Download data: FA, TXT

(Submitter supplied) Previous studies of appendage regeneration in the axolotl have shown that multiple genetic programs are modulated through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. more...

Organism:

Ambystoma mexicanum

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL14997

8 Samples

Download data: FA, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Ambystoma maculatum; Ambystoma mexicanum; Ambystoma andersoni

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

24 Samples

Download data: CEL

(Submitter supplied) Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. more...

Organism:

Ambystoma maculatum; Ambystoma mexicanum; Ambystoma andersoni

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21473 GPL25395 GPL25396

18 Samples

Download data: FA, TXT

(Submitter supplied) Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by array

Platform:

GPL25286

6 Samples

Download data: CEL

(Submitter supplied) Identifying the genetic program that induces limb regeneration in salamanders is an important resource for regenerative medicine, which currently lacks tools to promote regeneration of functional body structures. The genetic network underlying limb regeneration has been elusive due to the complexity of the injury response that occurs concomitant to blastema formation. Here we performed parallel expression profile time courses of non-regenerative lateral wounds versus amputated limbs in axolotl. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by array

Platform:

GPL15342

80 Samples

Download data: TXT

(Submitter supplied) Salamander limb regeneration is dependent upon tissue interactions that are local to the amputation site. Communication among limb epidermis, peripheral nerves, and mesenchyme coordinate cell migration, cell proliferation, and tissue patterning to generate a blastema, a mass of progenitor cells that forms missing limb structures. An outstanding question is how molecular cross-talk between these tissues gives rise to the regeneration blastema. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by array

Platform:

GPL15153

44 Samples

Download data: CEL

(Submitter supplied) An outstanding mystery in biology is why some species, such as the axolotl, can regenerate tissues whereas mammals cannot1. Here, we demonstrate that rapid activation of protein synthesis is a unique feature of the injury response critical for limb regeneration in the axolotl (Ambystoma mexicanum). By applying polysome sequencing, we identify hundreds of transcripts, including antioxidants and ribosome components that are selectively activated at the level of translation from pre-existing messenger RNAs in response to injury. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30838

18 Samples

Download data: TXT

(Submitter supplied) Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we identified expression patterns that explain PD duplication including upregulation of proximal homeobox gene expression and silencing of distal-associated genes whereas limb truncation was associated with disrupted skeletal differentiation. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by array

Platform:

GPL15153

12 Samples

Download data: CEL

(Submitter supplied) We know little about the control of positional information (PI) during axolotl limb regeneration which ensures that the limb regenerates exactly what was amputated and the work reported here investigates this phenomenon. Retinoic acid administration changes the PI in a proximal direction so that a complete limb can be regenerated from a hand. Rather that identifying all the genes altered by RA treatment of the limb, we have eliminated many off-target effects by using retinoic acid receptor selective agonists. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27159

12 Samples

Download data: FA, GFF, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15553

123 Samples

Download data: MTX, TSV

(Submitter supplied) Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15553

58 Samples

Download data: TXT, XLSX

(Submitter supplied) Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15553

60 Samples

Download data: TXT, XLSX

(Submitter supplied) Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15553

5 Samples

Download data: MTX, TSV