Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

PROVIDER: PRJNA374579 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5251430.fastq.gz	Fastqsanger.gz
	SRR5251440.fastq.gz	Fastqsanger.gz
	SRR5251431.fastq.gz	Fastqsanger.gz
	SRR5251441.fastq.gz	Fastqsanger.gz
	SRR5251432.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 17

Similar Datasets

Danio rerio

Project description:microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues

| PRJNA321321 | ENA

Danio rerio

Project description:mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues

| PRJNA321312 | ENA

mRNA and miRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues

Project description:mRNA and miRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues

| PRJNA321317 | ENA

The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq]

Project description:Pigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only contribute to assisted reproduction technologies of pigs but also will shed light into early human development. We generated 3D chromatin profiles for pig somatic cells, IVF, PA and AG preimplantation embryos. We found that the chromosomes in the pig preimplantation embryos are enriched for superdomains, i.e., the larger than 10M compartment domains, which are much rarer in mice. Wheras, p(s) curves, compartments and TADs, are largely conserved in somatic cells, and are gradually establishing during preimplantation embryogenesis. In the uniparental pig embryos, the establishment of chromatin architecture was highly asynchronized at all levels from IVF embryos, and a remarkably strong decompartmentalization was observed during zygotic genome activation (ZGA). Finally, chromosomes originating from oocytes always establish TADs faster than chromosomes originating from sperm, both before and during ZGA.

2020-07-02 | GSE153451 | GEO

Transcriptome-wide analysis of small RNA expression in early zebrafish development

Project description:During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the 5' and 3' ends of miRNAs with a large number of extra nucleotides added in a non-template directed manner. We also identified a large and diverse set of piRNAs expressed during early development, far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through-put sequencing

2012-03-01 | E-GEOD-27722 | biostudies-arrayexpress

5-formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming

Project description:5-methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. We identify this chromocenter as the perinucleolar compartment, a structure associated with RNA Pol III transcription. In Xenopus embryos, 5fC is highly enriched on Pol III target genes activated at ZGA, notably at oocyte-type tandem arrayed tRNA genes. By manipulating Tet and Tdg enzymes, we show that 5fC is required as a regulatory mark to promote Pol III recruitment as well as tRNA expression. Concordantly, 5fC modification of a tRNA transgene enhances its expression in vivo. The results establish 5fC as an activating epigenetic mark during zygotic reprogramming of Pol III gene expression.

2024-08-29 | GSE226467 | GEO

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [ATAC-seq]

Project description:Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.

2022-01-04 | GSE168361 | GEO

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [ChIP-seq]

2022-01-04 | GSE168360 | GEO

Identification of circulating miRNAs in a mouse model of nerve allograft transplantation under FK506 immunosuppression by Illumina small RNA deep sequencing

Project description:This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation.

2014-08-22 | GSE60624 | GEO

The dynamics and functional impact of transfer RNA repertoires during the maternal to zygotic transition in zebrafish

Project description:Embryogenesis entails dramatic shifts in mRNA translation and turnover to account for gene expression differences during proliferation and cellular differentiation. Codon identity modulates mRNA stability during early vertebrate embryogenesis, but how the composition of tRNA pools adapts to the embryo s translational demand is unknown. By quantitatively profiling the tRNA repertoires of zebrafish embryos during the maternal-to-zygotic transition, here we find that maternal and zygotic tRNA pools are distinct. We show that translational activation during embryogenesis and tRNA gene derepression are temporally coordinated by TORC1 activity, which increases at gastrulation and inactivates the RNA polymerase III repressor Maf1a/b in vivo. Reshaping of tRNA pools results in differential tRNA anticodon supply, but these changes do not alter decoding rates in zebrafish embryos. Instead, our data indicate that tRNA repertoires reflect the inherent codon bias of the zebrafish mRNA transcriptome, and tRNA levels are boosted at gastrulation to ensure efficient translation as embryos enter differentiation.

2024-02-26 | MSV000094166 | MassIVE

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