GEO DataSets

(Submitter supplied) Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

24 Samples

Download data: CEL, CHP

(Submitter supplied) Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platforms:

GPL530 GPL531

4 Samples

Download data: TXT

(Submitter supplied) Using genome-wide transcriptional profiling and whole-mount expression analyses of zebrafish larvae, we have identified hyaluronan synthase 3 (has3) as an upregulated gene during caudal fin regeneration. has3 expression is induced in the wound epithelium within hours after tail amputation, and its onset and maintenance requires fibroblast growth factor, phosphoinositide 3-kinase, and transforming growth factor-β signaling. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14607

9 Samples

Download data: PAIR

(Submitter supplied) Photoreceptor damage in adult mammals results in permanent cell loss and glial scarring in the retina. In contrast, adult zebrafish can regenerate photoreceptors following injury. By using a stable transgenic line in which GFP is driven by the cis-regulatory sequences of a glial specific marker gfap, Tg(gfap:GFP)mi2002, previous studies showed that Müller glia, the radial glial cells in the retina, proliferate after photoreceptor loss and give rise to neuronal progenitors that eventually differentiate into regenerated photoreceptors. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

15 Samples

Download data: CEL, TXT

(Submitter supplied) In zebrafish, vitellogenic oocytes can incorporate significant amounts of 17β-estradiol released from nearby granulosa cells according to a first-order kinetics, since the steroid low polarity ensures high permeability and affinity for yolk lipids. Estrogen bioactivity is likely, because the maternal mRNA for the estrogen receptor-β2 (ers2a) is highly expressed in ovulated oocytes. This transcript is available for translation in the embryo until its sharp decline from 4 to 8 hours post-fertilization (hpf), being replaced by low levels of zygotic ers2a mRNA from 24 hpf to hatching at 48 hpf, as determined by qRT-PCR. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6457

2 Samples

Download data: TXT

(Submitter supplied) To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration, we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout (mTOR-KO) transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover, mTOR was essential for the activation of macrophages, which is a key factor in maintaining the regenerative repair process. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: XLSX

(Submitter supplied) We examined the transcriptional effect of preventing cardiac contraction in zebrafish embryos which can be deprived of circulation without experiencing hypoxia since the fish obtain sufficient oxygen via diffusion. Morpholino antisense knockdown of cardiac troponin T2 (tnnt2) prevented cardiac contraction without affecting vascular development. We concluded that absence of hemodynamic force induces endothelial CXCR4a up-regulation and promotes recovery of blood flow. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

18 Samples

Download data: CEL, TXT, XLS

(Submitter supplied) Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: MTX, TSV

(Submitter supplied) Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24788

12 Samples

Download data: XLSX

(Submitter supplied) Exposures to dioxin, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) cause a wide array of toxicities in vertebrates and is mostly considered to be mediated through the inappropriate activation of the aryl hydrocarbon receptor (Ahr) signaling pathway. Although transcriptional regulation by Ahr is widely studied, the molecular mechanisms responsible for the adverse outcomes after Ahr activation are largely unknown. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

12 Samples

Download data: CEL, CHP

(Submitter supplied) Microarray analysis of 72h 1mM Galanthamine hydrobromide treated embryos. At this concentration GAL causes myopathology without causing morbidity.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL4603

1 Sample

Download data: TAR, TXT

(Submitter supplied) Planarian flatworms regenerate their heads and tails from anterior or posterior wounds and this blastema regeneration polarity is controlled by Wnt/β-catenin signaling. It is well known that a regeneration blastema of appendages of vertebrates such as fish and amphibians grows distally. However, it remains unclear whether a regeneration blastema in vertebrate appendages can grow proximally. Here, we show that a regeneration blastema in zebrafish fins can grow proximally along the proximodistal axis by calcineurin inhibition. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

7 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) Adult zebrafish can completely regenerate their caudal fin following amputation. This complex process is initiated by the formation of an epithelial would cap over the amputation site by 12 hours post amputation (hpa). Once the cap is formed, mesenchymal cells proliferate and migrate from sites distal to the wound plane and accumulate under the epithelial cap forming the blastemal structure within 48 hpa. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS1797

Platform:

GPL1319

18 Samples

Download data: CEL

Analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposed caudal fins at various time points up to 5 days post amputation. TCDD prevents caudal fin regeneration. Results provide insight into the pathways required for fin regeneration and the mechanisms of TCDD toxicity.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 2 agent, 3 time sets

Platform:

GPL1319

Series:

GSE3667

18 Samples

Download data: CEL

(Submitter supplied) Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals, for example, flatworms, newts, salamanders, and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately, the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues, and even cause serious loss of function or death. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL21741

9 Samples

Download data: FA, TXT

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

Organism:

Danio rerio

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL15180

7 Samples

Download data: TSV, TXT

(Submitter supplied) We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

Download data: TSV