GEO DataSets

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

Organism:

Mus musculus; Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

5 related Platforms

34 Samples

Download data: BED, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Danio rerio

Type:

Other

Platform:

GPL21741

3 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Mus musculus; Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21741 GPL20828

14 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Wound healing is impaired by infection; however, how microbe-induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe, Listeria monocytogenes, to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

9 Samples

Download data: RESULTS

(Submitter supplied) Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

39 Samples

Download data: CSV, LOOM, MTX, TSV

(Submitter supplied) Each organ of the human body requires locally-adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model, we reveal a molecular mechanism for brain-specific angiogenesis, that operates under the control of Wnt7a/b ligands, well-known blood-brain barrier maturation signals. The control mechanism relies on Wnt7a/b-dependent expression of Mmp25 in brain endothelial cells. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23274 GPL21741

3 Samples

Download data: TXT, XLSX

(Submitter supplied) This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

2 Samples

Download data: MTX, TSV

(Submitter supplied) Cypermethrin (CYP) and chlorpyrifos (CPF) are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish, which is non-target organisms. However, circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study, circRNAs were identified and characterized using RNA-seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21741

9 Samples

Download data: XLSX

(Submitter supplied) The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, LINEs, and LTRs, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: BW

(Submitter supplied) The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, LINEs, and LTRs, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: BW, TXT

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24995 GPL21741 GPL20828

52 Samples

Download data: BW

(Submitter supplied) The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, LINEs, and LTRs, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24995 GPL21741

14 Samples

Download data: BW, TXT

(Submitter supplied) The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins, and which exert non-overlapping functions. However, there is little information about ontogenetically distinct neutrophil populations. In this work, using a photoconvertible transgenic zebrafish line; Tg(mpx:Dendra2), we selectively label rostral blood island-derived and caudal hematopoietic tissue-derived neutrophils in vivo during steady state or upon injury. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

16 Samples

Download data: MTX, TSV

(Submitter supplied) To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we performed ATAC sequencing datasets of zebrafish spinal cord at 2 weeks after sham injury and after transection.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: BW

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

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: BW, TXT

(Submitter supplied) To identify regulators of spinal cord regeneration, we performed RNA sequencing of zebrafish spinal cord at 1 week after sham injury and after transection.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: TXT

(Submitter supplied) To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we performed ATAC sequencing datasets of zebrafish spinal cord at 1 week after sham injury and after transection.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: BW

(Submitter supplied) APC is a classical tumor suppressor in humans, and truncating mutations are early somatic events in most cases of sporadic colon cancer. APC directly enhances the activity of glycogen synthase kinase 3 (GSK-3) and therefore loss of full length APC reduces GSK-3 activity, leading to stabilization of b-catenin protein and activation of downstream Wnt/b-catenin signaling. GSK-3 also phosphorylates multiple core mRNA splicing factors and loss of Gsk3a/b in mouse ES cells and human lymphocytes alters mRNA splicing at a genome wide level. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: CSV

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL21741 GPL24776

62 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, TXT

(Submitter supplied) Retinoic acid (RA) functions as a ligand for the nuclear RA receptors (RARs), which regulate the expression of target genes by binding to RA response elements. RA signaling is required for multiple processes during chordate embryonic development, such as body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: BW, NARROWPEAK