GEO DataSets

(Submitter supplied) The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis.

Organism:

Lemur catta; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Danio rerio; Ateles sp.; Homo sapiens; Monodelphis domestica; Betapolyomavirus hominis; Ambystoma mexicanum; Gorilla gorilla; Pan troglodytes; Bos taurus; Rattus norvegicus; Gallus gallus; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1

Type:

Non-coding RNA profiling by array

Platforms:

GPL7724 GPL13686

7 Samples

Download data: 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) 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 mexicanum; Ambystoma andersoni; Ambystoma maculatum

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) The Mexican axolotl (Ambystoma mexicanum) is one member of a select group of vertebrate animals that has retained the amazing ability to regenerate multiple body parts. In addition to being an important model system for regeneration, the axolotl is also a leading model system for developmental biologists. Many genes used in development have been identified to be reused again during regeneration, however how this molecular circuitry is controlled during regeneration is unknown. more...

Organism:

Ambystoma mexicanum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20805

2 Samples

Download data: CSV

(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) 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) 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) Discovery of genes driving axolotl limb regeneration has been challenging due to limited genomic resources. We assembled 42 RNA-Seq samples totaling approximately 1.3 billion 100 base paired-end reads using Trinity (Grabherr M.G. et al, Nature Biotechnology, 2011; Haas B.J. et al, Nature Protocols, 2013): https://github.com/trinityrnaseq/trinityrnaseq/wiki). We created a transcriptome with complete sequence information for most axolotl genes, identified transcriptional profiles that distinguish blastemas from differentiated limb tissues, and uncovered functional roles for cirbp and kazald1 in limb regeneration.

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22800

42 Samples

Download data: TXT

(Submitter supplied) 10X sequencing of immune cells and limb regeneratesImmune cells are known to be critical for successful limb regeneration in the axolotl (Ambystoma mexicanum), but many details regarding their identity, behavior, and function are yet to be resolved. We isolated peripheral leukocytes from the blood of adult axolotls and then created two samples for single-cell sequencing: 1) peripheral leukocytes (N = 7,889) and 2) peripheral leukocytes with presumptive macrophages from the intraperitoneal cavity (N = 4,998). more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27159

4 Samples

Download data: FA, GTF, MTX, TSV

(Submitter supplied) MicroRNAs (miRNAs, miRs) modulate a multitude of cellular events. Here, we identify functional miRNA-protein networks that regulate human monocyte-derived dendritic cell (MDDC) differentiation. MiRNA profiling revealed stage-specific differential expression of 20 miRNAs during days 1, 3 and 5 of MDDC differentiation. To identify and prioritize miRNA-protein networks for functional validation, we developed a target ranking algorithm that incorporates many features of miRNA regulatory networks. more...

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Non-coding RNA profiling by array

Platform:

GPL4411

12 Samples

Download data: GPR

(Submitter supplied) Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-seq to generate transcript sequence data and identify 602 genes that are differentially expressed during limb regeneration. more...

Organism:

Bolitoglossa ramosi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24157

10 Samples

Download data: FA, TXT

(Submitter supplied) Humans and other tetrapods are considered to require apical-ectodermal-ridge, AER, cells for limb development, and AER-like cells are suggested to be re-formed to initiate limb regeneration. Paradoxically, the presence of AER in the axolotl, the primary regeneration model organism, remains controversial. Here, by leveraging a single-cell transcriptomics-based multi-species atlas, composed of axolotl, human, mouse, chicken, and frog cells, we first established that axolotls contain cells with AER characteristics. more...

Organism:

Ambystoma mexicanum

Type:

Other

Platform:

GPL27159

1 Sample

Download data: CSV, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Here, we developed a single-cell sequencing method based on combinatorial hybridization to generate a tissue-based transcriptomic landscape of the neotenic and metamorphosed axolotl. We performed gene expression profiling of over 1 million single cells across 19 tissues to construct the first adult axolotl cell landscape. Comparison of single-cell transcriptomes between the tissues of neotenic and metamorphosed axolotls revealed the heterogeneity of non-immune parenchymal cells in different tissues and established their regulatory network. more...

Organism:

Ambystoma mexicanum; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26363 GPL30541

615 Samples

Download data: TXT, XLSX

(Submitter supplied) We adopted a combinatorial hybridization based single-cell RNA-seq method to generate tissue based transcriptome atlas of adult axolotl and whole organism transcriptome atlas of larva axolotl. Gene expression profiling of over 1million single cells across 19 organs constructed the first adult axolotl cell atlas. Comparison between neoteny and metamorphosis organs revealed transcriptome heterogeneity of structural cells in different tissues and a sophisticated regulatory network. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30540

61 Samples

Download data: TXT

(Submitter supplied) Salamanders have the remarkable ability to functionally regenerate after spinal cord transection. In response to injury, GFAP+ glial cells in the axolotl spinal cord proliferate and migrate to replace the missing neural tube and create a permissive environment for axon regeneration. Molecular pathways that regulate the pro-regenerative axolotl glial cell response are poorly understood. Here we show axolotl glial cells up-regulate AP-1cFos/JunB after injury, which promotes a pro-regenerative glial cell response. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22800

12 Samples

Download data: XLSX