Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression in MZudu v. WT zebrafish gastrulae

ABSTRACT: We report RNA-sequencing data from zebrafish embryos lacking both maternal and zygotic expression of udu (which encodes Gon4l) (MZudu) at tailbud (TB) stage. Transcripts were compared to stage-matched wild-type (WT) embryos to identify differentially expressed genes.

ORGANISM(S): Danio rerio

PROVIDER: GSE96575 | GEO | 2017/09/13

SECONDARY ACCESSION(S): PRJNA379068

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Differential gene expression in WT v. MZoep-/- zebrafish gastrulae

Project description:We report RNA-sequencing data from zebrafish embryos lacking both maternal and zygotic expression of oep (which encodes Tdgf1) (MZoep-/-) at 90% epiboly stage. Transcripts were compared to stage-matched wild-type (WT) embryos to identify differentially expressed genes.

2020-05-18 | GSE147302 | GEO

Differential gene expression m39 vs. siblings

Project description:RNAseq analysis of cloche m39 mutant zebrafish embryos and wild type siblings at 90% epiboly - tailbud stage

2016-07-14 | GSE76690 | GEO

Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during maternal-to-zygotic transition and its relationship to zygotic genome activation

Project description:Upon fertilization, the embryonic genome remains transcriptionally inactive until the mid-blastula transition. Zygotic genome activation (ZGA) of vertebrate embryos has been extensively studied using nucleic acid-based strategies, but proteomics data are still scarce, impeding the full mechanistic understanding of how ZGA is executed during the maternal-to-zygotic transition (MZT). Here, we performed quantitative proteomics to decipher the proteome landscape of zebrafish embryos during the MZT, quantifying nearly 5,000 proteins across four embryonic stages. The stage-specific clustering based on protein expression pattern revealed that helicases (i.e., eif4a2 and ruvbl1) facilitate pluripotency factors (i.e., nanog, pou5f3, ctcf, and hmga1) triggering ZGA in zebrafish, accompanied by the maternal product decay with P-bodies and ubiquitin dependent proteolytic pathway. Dozens of transcription factors show wave-like expression patterns during MZT, implying their diverse functions in triggering the ZGA and modulating differentiation for organ development. The combination of morpholino knockdown and quantitative proteomics demonstrated that maternal Nanog is required for proper embryogenesis by regulating 1) interactions with other pluripotency factors, 2) F-actin band formation, 3) cell cycle checkpoints and 4) maternal product degradation. This study represents the most systematic proteomics survey of developmentally regulated proteins and their expression profiles accompanying MZT in zebrafish, which is a valuable proteome resource for understanding ZGA.

2024-05-01 | PXD036678 | Pride

Identification of Gon4l-associated genomic regions by DamID-seq

Project description:We report DNA adenine methyltransferase identification (DamID)-sequencing data to identify Gon4l-associated genomic regions in wild-type (WT) tailbud (TB) stage zebrafish embryos. Methylated, and therefore Gon4l-proximal, gDNA was isolated from embryos expressing a Gon4l-Dam fusion and compared to that from embryos expressing GFP-Dam control.

2017-09-13 | GSE96576 | GEO

Expression data from early Zebrafish embryos after knockdown of mir-34

Project description:microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied. We used microarrays to detail the effect of maternal microRNA mir-34 in regulation of zygotic trancription during the initial stages of Zebrafish embryonic development from one cell stage through the maternal-zygotic transition up to 24 hours post fertilization. Zebrafish embryos were selected at specific stages of early embryonic development (1, 7, and 24 hours post fertilization). RNA was extracted and hybridized to Affymetrix microarrays. The embryos were injected with anti-microRNA LNA and were kept for constant monitoring for the indicated time points. A mockLNA was injected as a control. The embryos were visualized for any visible developmental abnormalities.

2013-04-03 | E-GEOD-32360 | biostudies-arrayexpress

Nanog affects establishment of chromatin marks at zebrafish Zygotic Genome Activation

Project description:In zebrafish embryos, the maternal transcription factors (TFs)Nanog, Pou5f3 and Sox19b activate the early zygotic gene expression. To evaluate the role of Nanog, we examined the changes in H3K27ac and H3K4me3 chromatin modifications in the MZnanog embryos mutant by maternal and zygotic Nanog.

2020-05-07 | GSE143439 | GEO

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition

Project description:During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNAbound proteome. This protein constellation consists of many conserved RBPs, with additional embryo- and stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of RBPs in embryogenesis, we focused on hnRNP A1. iCLIP and subsequent mRNA reporter assays revealed a function for hnRNP A1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3’UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that hnRNP A1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-miR-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of hnRNP A1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that hnRNP A1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.

2017-03-27 | PXD006098 | Pride

Transcriptome analysis of wild-type and maternal ybx1 mutant zebrafish embryos during early development

Project description:To study the function of zebrafish Ybx1 during early embryogenesis, we generated maternal ybx1 (Mybx1) mutant using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic loss of maternal mRNA decay and zygotic genome activation in Mybx1 embryos during maternal-to-zygotic transition.

2018-09-01 | GSE108924 | GEO

Transcriptome analysis of wild-type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development

Project description:To study the function of zebrafish nuclear pores during early embryogenesis, we generated maternal zygotic double mutant of nup85;nup133 (MZnup85;nup133) using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal-to-zygotic transition.

2023-03-04 | GSE146394 | GEO

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition

Project description:We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal-to-zygotic transition

2017-03-24 | GSE76212 | 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