Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis

ABSTRACT: To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing.

ORGANISM(S): Danio rerio

PROVIDER: GSE52652 | GEO | 2014/09/30

SECONDARY ACCESSION(S): PRJNA229539

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis

Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing. Whole transcriptome sequencing (RNA-seq) was performed on zebrafish rx3-/- mutants, wild-type siblings and wild-type AB strains at 13 hpf

2014-09-30 | E-GEOD-52652 | biostudies-arrayexpress

RNA-Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers

Project description:In this study, we performed RNA-seq on 5 dpf livers of uhrf1-hi272 mutants and phenotypically wild-type siblings collected at 120 hpf.

2020-12-01 | GSE160710 | GEO

Danio rerio

Project description:Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis

| PRJNA229539 | ENA

Yap and Taz regulate retinal pigment epithelial cell fate

Project description:The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.

2015-08-06 | E-GEOD-71681 | biostudies-arrayexpress

Transcriptional analysis of forebrain plus optic cup from zebrafish embryos after BMP4 overexpression

Project description:Forebrain and optic cups were microdissected from zebrafish embryos at 21 hours post-fertilization (hpf) after heat-shock at 15 hpf to induce overexpression of BMP in heterozygous tg(hsp70l:bmp4) embryos vs wild type controls.

2021-04-26 | E-MTAB-10085 | biostudies-arrayexpress

DNA methylation analysis by RRBS of WT and uhrf1-hi272 mutant zebrafish whole larvae at 5 dpf

Project description:DNA methylation is a central repressive epigenetic mark. In this dataset we performed RRBS on whole zebrafish larvae from uhrf1-hi272 mutants and phenotypically wild-type siblings to determine which genomic regions have changes in DNA methylation due to uhrf1 loss.

2020-12-01 | GSE160706 | GEO

Transcriptome profiling of zebrafish optic fissure fusion

Project description:Incomplete fusion of the optic fissure leads to ocular coloboma, a congenital eye defect that affects up to 7.5 per 10,000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before (32 hours post fertilisation, hpf), during (48 hpf) and after (56 hpf) optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT-PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a (ntn1a) as highly differentially expressed across optic fissure fusion, with a resultant ocular coloboma phenotype following morpholino antisense translation-blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies, we have generated an online open-access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma.

2020-10-22 | GSE159822 | GEO

Transcriptomic profiling of the liver from dnmt1 mutant zebrafish larvae compared to their phenotypically normal siblings at 120 hpf

Project description:In this dataset we performed RNA-seq on pools of livers dissected at 120 hpf from dnmt1(s904) mutants and phenotipically wild-type looking siblings.

2020-12-01 | GSE160726 | GEO

Transcriptomic profiling of the liver from dnmt1 mutant zebrafish larvae compared to their phenotypically normal siblings at 120 hpf

Project description:Transcriptomic profiling of the liver from dnmt1 mutant zebrafish larvae compared to their phenotypically normal siblings at 120 hpf

| PRJNA674308 | ENA

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

Project description:Purpose: To identify differential expressed genes for loss of function of Mycn in zebrafish Methods: wild-type and mycn mutant zebrafish embryos were collected for RNA sequencing at 48 hpf (hours post fertilisation) and 72 hpf Results: We found 85 (overlapped) down-regulated genes in mycn mutant embryos at 48 hpf and 72 hpf (padj < 0.1, log2 fold change < 0) Conclusions: 85 down-regulated genes were identified

2021-12-17 | GSE191001 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data