Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (ChIP-chip)

ABSTRACT: The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the mbryo derived ZF4 cell line. Specifically, we determined teh enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, and pathway analysis.

ORGANISM(S): Danio rerio

PROVIDER: GSE23691 | GEO | 2011/02/08

SECONDARY ACCESSION(S): PRJNA133135

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (ChIP-chip)

Project description:The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the mbryo derived ZF4 cell line. Specifically, we determined teh enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, and pathway analysis. ChIP-chip experiments were performed from duplicate cultures

2011-02-08 | E-GEOD-23691 | biostudies-arrayexpress

Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (Gene expression)

Project description:The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the embryo derived ZF4 cell line. Specifically, we determined the enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, pathway analysis, and in relation to gene expression.

2011-02-08 | GSE23679 | GEO

Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (Gene expression)

Project description:The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the embryo derived ZF4 cell line. Specifically, we determined the enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, pathway analysis, and in relation to gene expression. Gene expression experiments were performed on three biological replicates.

2011-02-08 | E-GEOD-23679 | biostudies-arrayexpress

Transcription profiling of zebrafish ZF4 and PAC2 cell lines cultured in medium with or without FCS

Project description:In this study, zebrafish ZF4 and PAC2 cells were seeded in 0.5% or 1% FCS, respectively, and grown to 85% confluence and subsequently cultured for 24 hours without serum. Then they were treated with either medium without serum or medium with serum (ZF4 in 10% FCS and PAC2 in 15% FCS).After 6 hours, RNA was extracted from the cells and analyzed using the Affymetrix GeneChip Zebrafish Genome Array (GeneChip 430). There are 15502 oligonucleotide sets on each Affymetrix chip, 14895 of which can be linked to a UniGene assignment (Unigene data set 06-12-2005).

2006-06-12 | E-MEXP-736 | biostudies-arrayexpress

Chromatin immunoprecipitation of three PcG proteins and of histone H3 trimethylated at Lys 27 in Drosophila

Project description:We determined the distribution of three PcG proteins: PC, PSC and E(Z), and of histone H3 trimethylated at Lys 27 by chromatin immunoprecipitation (ChIP) coupled with analysis of immunoprecipitated DNA with a high density genomic tiling microarray (Affymetrix).

2006-12-30 | E-MEXP-535 | biostudies-arrayexpress

DNA methylome patterns of zebrafish cells under cold pressure

Project description:In this study, MeDIP-seq and RNA-seq were performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cell line (ZF4) and its variation under cold environment.This study puts a new insight into the genome-wide epigenetic regulation under cold environment. ZF4 cells were cultured at 28 Â°C as control and at 18 Â°C for 5 days and 30 days, seperately. Each condition has three biological replica.

2016-07-30 | E-GEOD-71567 | biostudies-arrayexpress

WNT pathway activation promotes phenotypic reprogramming of glioblastoma derived cells in zebrafish nervous system microenvironment

Project description:phenotypic reprogramming ability of teh zebtafish brain microenviroment on GBM derived cells controlled by the activation of endogenous Wnt pathway Class comparison between different time point of human GBM cells trasplanted into zebrafish

2013-02-28 | E-GEOD-25012 | biostudies-arrayexpress

DNA methylome patterns of zebrafish cells under cold pressure

2016-07-30 | GSE71567 | GEO

Danio rerio

Project description:Effects of rapamycin exposure on zebrafish ZF4 cells

| PRJNA230818 | ENA

Quantitative Analysis of ZF4 cells Transcriptomes when Infected with Edwardsiella tarda

Project description:Edwardsiella tarda is a Gram-negative bacterial pathogen that can infect a wide range of freshwater and marine fish. However, the immune evasion mechanisms of Edwardsiella tarda is not fully understood. We found that Edwardsiella tarda infection generally significantly upregulated and downregulated a lot of immune-related genes of zebrafish ZF4 cells using RNA-seq technology.

2017-02-14 | GSE81773 | 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