GEO DataSets

(Submitter supplied) Cerebral cavernous malformations (CCMs) are anomalies that develop mainly in the cerebral vasculature. They result from mutations in CCM1/KRIT1, CCM2, or CCM3/PDCD10. Loss of CCM proteins triggers a MAPK-Krüppel-like factor 2 (KLF2) signaling cascade, which induces a pathophysiological pattern of gene expression within endothelial cells. The downstream target genes that are activated by KLF2 are mostly unknown. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

12 Samples

Download data: BW

(Submitter supplied) hand2 reporter-expressing cardiac cells fail to migrate to the midline. To investigate the underlying molecular changes, we sequenced mRNA from 3900 and 3836 hand2 reporter-expressing single cells from 24 hpf hand2 FLD-/- and hand2 FLD+/? sibling embryos, respectively. Furthermore, hand2 is broadly expressed within the LPM, which gives rise to various cell lineages and tissues including the cardiovascular system, blood, kidneys, mesothelium, and limb connective tissue. more...

Organism:

Danio rerio

Type:

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

Platforms:

GPL20828 GPL25922

8 Samples

Download data: BW, TAR

(Submitter supplied) Despite extensive studies on endogenous heart regeneration within the past 20 years, the players involved in initiating early regeneration events are far from clear. Here, we assessed the function of neutrophils, the first-responder cells to tissue damage, during heart regeneration. We detected rapid neutrophil mobilization to the injury site after ventricular amputation, peaking at 1-day post-amputation (dpa) and resolving by 3 dpa. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) Hundreds of human mutations are linked to autism and related disorders, yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein-truncating mutations or patient-specific missense variants corresponding to autism-risk alleles in 17 human genes. We observed baseline and stimulus-driven behavioral changes at larval stages, as well as social behavior differences in lines tested as juveniles. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24995 GPL25922

104 Samples

Download data: CSV, TAB

(Submitter supplied) The antimicrobials isoniazid and pyrazinamide, used for the treatment of tuberculosis are known to cause drug-induced liver injury in humans. This limits the effectiveness of tuberculosis treatment, resulting in incomplete cure, relapse and the development of antimicrobial resistance. MicroRNAs are known to be good biomarkers of disease, with the microRNA miR-122 being diagnostic for liver injury. In this study zebrafish larvae were exposed to the anti-tuberculosis drugs isoniazid and pyrazinamide at concentrations which demonstrated liver injury by microscopy and histology. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25922

24 Samples

Download data: FA

(Submitter supplied) This study was carried out to compare the changes in gene expression in livers of 120 hpf control sibling and mutant uhrf1-hi272 zebrafish larvae in response to treatment with DMSO or Palbociclib (PD)

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

18 Samples

Download data: TXT

(Submitter supplied) This study was carried out to compare the changes in basal gene expression in livers of ~1 year old zebrafish adults in response to whole body mutation of the arsenite methyltransferase gene (as3mt) - 8 bp deletion in exon 3 resulting in a loss of function.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

8 Samples

Download data: TXT

(Submitter supplied) Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: CSV, RDS

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

3 Samples

Download data: MTX, TSV

(Submitter supplied) As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

40 Samples

Download data: TXT

(Submitter supplied) This study was carried out to compare the changes in gene expression in whole larvae 120 hours post fertilization zebrafish larvae in response to whole body mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 6-120 hpf exposure to 1 mM sodium arsenite (iAs).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

12 Samples

Download data: TXT

(Submitter supplied) This study was carried out to compare the changes in gene expression in 5 dpf zebrafish larval livers in response to mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 1 mM sodium arsenite treatment (96-120 hpf)

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

20 Samples

Download data: TXT

(Submitter supplied) Overexpression of high levels of human UHRF1 tagged with EGFP (hUHRF1-EGFP)high in zebrafish hepatocytes induces cellular senescence by 5 days post fertilization (dpf) and hepatocellular carcinoma by 15-20 dpf. The goal of this study is to compare the transcriptome profile of zebrafish livers with (hUHRF1-EGFP)high overexpression compared to WT siblings. RNAseq was performed on RNA extracted from pools of microdissected liveres by using RiboZero libary prep to capture all transcripts, including transposable elements, that are expressed in the livers.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

11 Samples

Download data: TXT

(Submitter supplied) Homozygosity for the Z allele of α1-antitrypsin (ZAAT) predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum (ER) of hepatocytes, resulting in gain-of-function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency, suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

24 Samples

Download data: CSV

(Submitter supplied) The functional jaw is composed of multiple connective tissues including skeletal components (bone, cartilage, and teeth), tendon, ligament, and musculature. Cranial neural crest-derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved, we profile multi-omic chromatin accessibility (snATACseq) and transcriptome (snRNAseq) of jaw mesenchyme at single-cell resolution from the developing zebrafish jaw.

Organism:

Danio rerio

Type:

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

Platforms:

GPL21741 GPL25922

4 Samples

Download data: H5

(Submitter supplied) Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here, we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non-cranial neural crest lineage cells (including skin and immune populations) in the first 3 days after ligament injury.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

10 Samples

Download data: MTX, TSV

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25922 GPL21741

10 Samples

Download data: MTX, TSV