Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

ABSTRACT: Here we describe successful implementation of CUT&Tag for profiling protein-DNA interactions in zebrafish embryos. We optimized CUT&Tag protocol to generate high resolution maps of enrichment for the histone variant H2A.Z during zebrafish development. We were able to establish dynamics of H2A.Z genomic patterning from shield stage to 24hpf embryos. Our work demonstrates the power of combining CUT&Tag with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

ORGANISM(S): Danio rerio

PROVIDER: GSE178559 | GEO | 2022/02/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

2021-06-17 | GSE178343 | GEO

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

| PRJNA738523 | ENA

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

| PRJNA739658 | ENA

Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing

Project description:In this study, single cell sequencing technique was utilized to explore the transcriptomes of zebrafish PGCs in three time points: 6hpf (shield stage), 11hpf (3-somite stage) and 24hpf (prim-5 stage).

2019-02-01 | GSE122208 | GEO

RNA-seq of HNRNPAB morpholino in zebrafish

Project description:To investigate the transcriptomic alterations following 24hpf knockdown of the gene HNRNPAB in zebrafish, we injected HNRNPAB morpholino with 3ng and 6ng into 1-cell zebrafish embryos separately, and the 24hpf embryos were collected for RNA-seq.

2022-03-31 | GSE199586 | GEO

CUT&RUN profiling of Tfap2a binding genome-wide using zebrafish embryos at 24hpf

Project description:CUT&RUN profiling of Tfap2a binding genome-wide using zebrafish embryos at 24hpf

| PRJNA1054088 | ENA

CUT&Tag for H2A.Z using mouse heart tissues from control and Znhit1-deficient mice

Project description:Znhit1 is an important subunit of the SRCAP complex, which regulates gene transcription by replacing histone H2A with a variant H2A.Z at gene promoter regions. Deletion of Znhit1 has also been reported to impact the incorporation of H2A.Z in genome. To explore the function of Znhit1 in heart tissues, we performed CUT&Tag assays for H2A.Z to examine the distribution changes of H2A.Z on the genome.

2022-04-19 | GSE194162 | GEO

Cut&Tag of ZGA staged embryos

Project description:Cut&Tag of ZGA staged embryos

| PRJNA724739 | ENA

CUT&RUN profiling of Tfap2a binding genome-wide using zebrafish embryos at 24hpf

Project description:The purpose of this study was to identify Tfap2a binding genome-wide in zebrafish embryos at 24hpf. Tfap2 transcription factors are essential regulators of neural crest development, melanocyte differentiation, and melanoma progression. We aimed to identify Tfap2a-occupied genes to determine direct Tfap2a-regulated transcriptional networks.

2023-12-18 | GSE250450 | GEO

CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)

Project description:Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during adult fin regeneration in zebrafish. Data generated from our protocol recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and H3K4me3 is lost at genes which become silenced . Interestingly, these epigenetic reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24 hour old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.

2024-05-01 | GSE261538 | GEO

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