Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling Zebrafish Sap130b gene mutations in embryogenesis

ABSTRACT: This study profiled the transcriptome of zebrafish embryos harboring mutation in the Sin3A associated Protein 130b (sap130b) gene at 36 hours post fertilization (hpf). The sap130b mutant was generated via Cas9 mediated gene editing. Zebrafish sap130b mutants are viable and survive as adults with no observable phenotype. Maternal Zygotic sap130b mutants were established and they were also normal and it was reasoned that sap130a was compensating for the loss of sap130b. A transcriptome analysis was performed at 36 hpf to compare with our analysis of sap130a at this stage.

ORGANISM(S): Danio rerio

PROVIDER: GSE228450 | GEO | 2023/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome profiling Zebrafish Sap130a gene mutations in embryogenesis

Project description:This study profiled the transcriptome of zebrafish embryos harboring mutation in the Sin3A associated Protein 130a (sap130a) gene at 36 hours post fertilization (hpf). The sap130a mutant was generated via Cas9 mediated gene editing. Zebrafish sap130a mutants are viable presumable due to the presence of maternal RNA. Generation of maternal zygotic (MZ) mutants resulted in an incomplete penetrance of heart ventricle defects that were visible as early as 36 hpf. In this experiment the MZsap130a mutant embryos were further sorted for embryos with smaller ventricle (SV) vs normal size ventricle (NV). To extend on this study and to specifically analyze the heart, sap130a mutant and WT hearts at 48 hpf were extracted for RNA-seq analysis.

2023-05-31 | GSE228057 | GEO

The Translation Initiation Factor eIF3h Targets Specific Transcripts to Polysomes during Embryogenesis

Project description:We have sequenced the polysome-associated translating mRNAs from stage-matched wild-type and eif3ha morphant embryos at ~24 hpf stage to identify transcripts translationally regulated by eIF3ha. As a control, we have also sequenced total mRNAs from the stage-matched wild-type and eif3ha morphants as well at ~ 24 hpf. Polysome-associated mRNAs were isolated from 300 zebrafish embryos. Total RNA was isolated from 50 zebrafish embryos. Single 36-base pair reads were sequenced on the Illumina Genome Analyzer Iix.

2013-06-05 | E-GEOD-44584 | biostudies-arrayexpress

Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish

Project description:Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues, but their identification and organogenesis-related function have not elucidated. In this study, high-throughput sequencing was performed at three different organogenesis stages of zebrafish embryos, which were important for zebrafish muscle development. The three stages were 10 hpf (hours post fertilization) (T1), 24 hpf (T2) and 36 hpf (T3).

2023-07-19 | GSE235668 | GEO

Gene expression profile of zebrafish synpo2 mutant

Project description:Embryonic zebrafish synpo2 mutants were compared to wild-type (22 hpf)

2021-01-01 | GSE150046 | GEO

Excess glucose or fat differentially affects gene expression and appetite regulation during zebrafish embryogenesis

Project description:Zebrafish embryos were exposed to 3% glucose (24-72 hpf) and injected 2 nL of BODIPY-FL C12:0 dissolved in canola oil directly into the yolk sac at 24 hpf. At 72 hpf embryos were collected for analysis. Quantitative PCR analysis of glucose exposed embryos demonstrated that glucose exposure activates the insulin pathway while FFA/TAG injection activates the lipolysis and beta-oxidation pathways. At 72 hpf embryos were collected and bulk RNAseq was performed on control, glucose exposed and FFA/TAGs injected embryos.

2023-06-01 | GSE213859 | GEO

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

Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis

2014-09-30 | GSE52652 | GEO

Control of progenitor cell positioning and organ patterning during embryogenesis

Project description:The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step in organ development and function. Using primordial germ cells and the process of gonadogenesis as anÂ in vivoÂ model, we present the developmental mechanisms facilitating the maintenance of a motile progenitor cell population at the site where the organ develops. We find that the action of repulsive cues coupled with the generation of physical barriers confine the cells to the correct bilateral positions within the embryo. Using computer particle-based simulations we could also demonstrate the role of reflecting barriers, from which cells turn away upon contact, and the importance of proper level of cell-cell interaction for maintaining the tight cell clusters and their correct positioning at the target region. The cellular mechanisms operating during those events were determined using high-resolution live imaging microscopy. This analysis revealed cell polarity change upon interaction with the physical barrier and the establishment of compact clusters that involves increased cell-cell interaction as a result of collapse of cell protrusions and enhanced adhesion. The combination of these developmental and cellular RNA profiling in zebrafish embryos of 7 hpf and 36 hpf in sorted germ cells and randomly sorted somatic cells

2016-04-05 | E-GEOD-77077 | biostudies-arrayexpress

Zebrafish transcriptomics in 24 and 36 hpf embryos after knockdown of glucocorticoid receptor translation

Project description:To further characterize the roles of cortisol signaling via the glucocorticoid receptor (GR) in developing zebrafish, we have used morpholino oligonucleotides to knockdown GR protein translation and measured gene expression in RNA extracted from 24 and 36 hours post fertilization (hpf) embryos. The GR morpholino was characterized previously in Nesan et al., 2012, Endocrinology 181, 35-44) Single-cell zebrafish embryos were microinjected with either active morpholino or mispair control. Embryos were frozen at 24 and 36 hpf and total RNA extracted for microarray analysis. Three independent replicates (different breeding events on separate days) were performed for each treatment per timepoint.

2013-08-28 | E-GEOD-50376 | biostudies-arrayexpress

Single-cell transcriptomic analysis of 36 hpf Zebrafish etv2 and jam2b positive cells

Project description:We performed single-cell RNAseq analysis of FACs sorted etv2 and jam2b psoitive cells from etv2Gt(2A-Venus) ; jam2bGt(2A-Gal4);UAS:NTR-mCherry zebrafish embryos at 36 hpf using 10x Genomics' Chromium platform. 18 distinct cell populations were identified including vascular endothelial cells and LPM cells.

2021-07-13 | GSE179926 | 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