Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of zebrafish early somites

ABSTRACT: The segmented pattern of the vertebral column and musculature in vertebrate embryos is established during somitogenesis. Here, using the model animal zebrafish, we employed Data-Independent Acquisition (DIA) to capture the proteomics change at the early stages of somite development.

INSTRUMENT(S):

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Embryo, Somite

SUBMITTER: Guangyu SUN

LAB HEAD: Guangyu Sun

PROVIDER: PXD058516 | Pride | 2025-10-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20230615_SGY_SG-A2.raw	Raw
	20230615_SGY_SG-A3.raw	Raw
	20230615_SGY_SG-A4.raw	Raw
	20230615_SGY_SG-C1.raw	Raw
	20230615_SGY_SG-C2.raw	Raw

Items per page:

1 - 5 of 18

Publications

Actn4 Links Inactive Integrin α5 With Actin in Zebrafish Somites.

Sun Guangyu G Holley Scott A SA

Molecular & cellular proteomics : MCP 20251008 2

Integrins are key plasma membrane proteins that mediate cell-ECM adhesion and communication, and they rely on a conformational change for their activation and bidirectional signaling. However, there are few in vivo studies of integrin activation. Here, we identify Integrin α5 (Itgα5)-associated proteins in the physiological setting of zebrafish somite morphogenesis. Using label-free mass spectrometry, we compared Itgα5-associated proteins in different integrin activation states. As expected, we ...[more]

PMID: 41072919

Similar Datasets

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-02-13 | E-GEOD-52706 | biostudies-arrayexpress

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MeDIP-seq)

Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MeDIP profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.

2015-02-13 | E-GEOD-52703 | biostudies-arrayexpress

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MRE-seq)

Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MRE profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.

2015-02-13 | E-GEOD-52704 | biostudies-arrayexpress

Zebrafish embryo Kac - Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos

Project description:Zebrafish (Danio rerio) model system have used widespread vertebrate investigations for genetic and cell biological analyses, and is suitable for small molecular screens such as chemical, toxicity and drug in order to use for human diseases and drug discovery . Recently, These powerful zebrafish model increasingly apply to human metabolic disease such as obesity and diabetes and toxicology. Despite a lot of advantages, proteomics research at zebrafish has received little interest in comparison with genetic and biological research using histology and in situ hybridization. Protein lysine acetylation is one of the most known post-translational modifications with dynamic and reversibly controlled by lysine acetyltransferase such as histone acetyltransferases and lysine deacetylase such as histone deacetylases and sirtuins family.Also, during the past year, global lysine acetylome studies using MS-based proteomics approach was in diverse species such as human, mouse, E. coli, Yeast and plants. Based on global acetylome data, our understanding of the roles of lysine acetylation in various cellular processes has increased. . The aim of this study was to identify Lysine acetylation in zebrafish embryos and determine the homology from Human at modified site level. Here we showed the global lysine acetylation study in Zebrafish embryos using MS-based zebrafish embryos.

2016-10-10 | PXD003455 | Pride

Zebrafish embryo_phosphorylation_18O labeling

Project description:The zebrafish (Danio rerio) is a popular animal model in studies of vertebrate development and organogenesis. Recent research has shown a similarity of approximately 70% between the human and zebrafish genomes and of 84% in human disease-causing genes, specifically. Zebrafish embryos have a number of desirable features, including transparency, a large size, and rapid embryogenesis. Protein phosphorylation is a well-known post-translational modification (PTM), which performs various biological functions. Recent mass spectrometry (MS) developments have enabled the study of global phosphorylation patterns by using MS-based proteomics coupled with TiO2 phosphopeptide enrichment. In the present study, we identified 3,500 non-redundant phosphorylation sites on 2,166 phosphoproteins and 1,564 quantified phosphoproteins in zebrafish embryos.

2015-10-14 | PXD002232 | Pride

Zebrafish 24hpf whole embryo MZezh2mutant

Project description:Polycomb group (PcG) proteins are transcriptional repressors important to maintain cell identity during embryonic development. Ezh2, the catalytic subunit of the Polycomb Repressive Complex 2, is responsible for placing the epigenetic repressive mark histone H3 lysine 27 trimethylation (H3K27me3). In contrast to results in mouse models, zebrafish embryos mutant for both maternal and zygotic ezh2 (MZezh2) can form a normal body plan at 1 day post fertilization (dpf) but die at 2 dpf, exhibiting pleiotropic phenotypes. To elucidate the specificity of PcG-mediated repression during early zebrafish development, we conducted in depth analysis of the transcriptome, epigenome, and proteome of the MZezh2 mutant embryos at 1 dpf. We found that, despite modifications in the epigenetic landscape, transcriptome and proteome analysis revealed only minor changes in gene and protein expression levels.

2019-09-09 | PXD010922 | Pride

Ciona savignyi notochord LC-MS/MS based on 4D Mass Spectromete

Project description:Lumen formation and inflation are crucial for tubular organ morphogenesis, yet the underling mechanism remains largely unrevealed. Here, we applied 4D proteomics to screen the lumenogenesis-related proteins and reveal the potentially biological pathways that are involved in lumen inflation during notochord lumen formation in ascidian Ciona savignyi.

2023-05-10 | PXD037089 | Pride

Zebrafish Deyolking Survey - A Survey of the Impact of Deyolking on Biological Processes Covered by Shotgun Proteomic Analyses of Zebrafish Embryos

Project description:Deyolking, the removal of the most abundant protein from the zebrafish (Danio rerio) embryo, is a common technique for in-depth exploration of proteome-level changes in vivo due to various environmental stressors or pharmacological impacts during embryonic stage of development. However, the effect of this procedure on the remaining proteome has not been fully studied. Here, we report a label-free shotgun proteomics survey on proteome coverage and biological processes that are enriched and depleted as a result of deyolking.

2015-10-14 | PXD002124 | Pride

Zebrafish early embryos isolated nuclei and whole blastomeres LC-MSMS

Project description:Nuclear pore complex (NPC) structure and maturity changed during early development before MBT in zebrafish embryos. Aiming to further confirm the difference of NPCs among different stages during MZT, we first isolated nuclei from 32-cell and 512-cell stage embryos as most zygotic genes have not been transcribed at these two stages yet. The lysates from identical number (about 12,500 nuclei per stage) isolated nuclei were then trypsin-digested and fractionated, followed by high-resolution LC-MS/MS analysis on the Q-Exactive HF-X mass spectrometers using a label-free assay. Whole blastomeres from 32-cell and 512-cell were also prepared with yolk removal to serve as total protein profile control, and the same amount lysates were analyzed by high-resolution LC-MS/MS with TMT labelled. Each sample for MS analysis had two repeats. Correlation analysis revealed that the abundance ratio from isolated Nuclei and whole deyolking balstomeres did not correlate well, but samples in Nuclei or Whole blastomeres were well correlated. This result indicates the convincible sample preparation as well as the variability in nuclei composition in early developmental period before MBT.

2023-08-25 | PXD017896 | Pride

Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes

Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo. Zic3 ChIP of wild type and sqet33 transgenic

2014-02-27 | E-GEOD-41458 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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