Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide DNA methylation of zebrafish livers at 120 hpf with hUHRF1-EGFP overexpression in hepatocytes

ABSTRACT: We investigated DNA methylation changes in preneoplastic zebrafish livers following hepatocyte-specific overexpression of the epigenetic regulator UHRF1. Genome-wide DNA methylation profiling was performed using low-input reduced representation bisulfite sequencing (RRBS) on pooled livers dissected from wild-type sibling larvae and Tg(fabp10a:hUHRF1-EGFP^high) zebrafish at 5 days post fertilization. Across all samples, approximately 10× coverage was achieved at more than 1.5 million CpG sites. These were compared to profiling carried out in parallel on wild-type samples present in GSE173792. Hepatocyte-specific hUHRF1 overexpression altered methylation levels at nearly one-third of all CpGs analyzed, with ~15% of CpGs exhibiting loss of methylation; hypomethylation occurred predominantly at CpGs that were fully methylated in controls, whereas CpGs that gained methylation were enriched among sites that were partially methylated in control livers. Analysis of WT samples was published in PMID: 34356097.

ORGANISM(S): Danio rerio

PROVIDER: GSE317475 | GEO | 2026/08/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Zebrafish liver: Tg(fabp10a:pt-beta-catenin) versus non-transgenic control siblings

Project description:To investigate mechanisms by which activated β-catenin signaling promotes liver tumor formation and to identify potential therapeutics for these cancers, we generated transgenic zebrafish expressing hepatocyte-specific activated β-catenin (Tg(fabp10a:pt-β-cat) zebrafish. As adults, these animals show increased liver size, decreased survival, and histologic abnormalities similar to human HCC. To further characterize our model, we used microarray analysis to compare gene expression in Tg(fabp10a:pt-β-cat) zebrafish livers to that of non-transgenic control sibling livers. This experiment includes 2 biological replicates. Each replicate represents one Tg(fabp10a:pt-beta-catenin) zebrafish compared to non-transgenic control sibling.

2015-04-30 | E-GEOD-68124 | biostudies-arrayexpress

Zebrafish liver: Tg(fabp10a:pt-beta-catenin) versus non-transgenic control siblings

2015-04-30 | GSE68124 | GEO

Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

Project description:The goal of this study is genomic chromatin accessibility of 120 hpf zebrafish livers by ATAC-Seq. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and the DNA methylation profile using reduced representation bisulfite sequencing (RRBS).

2021-07-07 | GSE173792 | GEO

Comparing the genome-wide chromatin accessibility of uhrf1 hi272 mutants and phenotypically wildtype whole zebrafish embryos at 120 hpf using ATAC-Seq.

Project description:The goal of this study is to study the chromatin accessibility differences between control and uhrf1 hi272 mutant 120 hpf zebrafish embryos (uhrf1 hi272+/-, Tg(fabp10a:CAAX-EGFP) using ATAC-Seq technique.

2020-06-23 | GSE151293 | GEO

Expression profiles of zebrafish transgenic line Tg(fabp10a:def)-I

Project description:We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a. We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line. Total RNA from the adult livers of three independent batches of 3-month-old Tg(fabp10a:def)-I and wild type (AB strain) male fish was extracted using TRIzol (Invitrogen), each batch with the liver samples from three fish mixed together. The samples were subjected to microarray hybridization and the data were generated for further analysis.

2013-02-28 | E-GEOD-41059 | biostudies-arrayexpress

Differential gene expression in the liver of zebrafish larvae exposed to 1 mM inorganic arsenic from 4-120 hpf

Project description:The goal of this study is to compare gene expression levels in the livers of larval Tg(fabp10:nls-mcherry) exposed to 1 mM inorganic arsenic from 4-120 hpf to the unexposed siblings. Samples were collected from Tg(fabp10:nls-mcherry) zebrafish larvae that were derived from incrossed parents of the same strain. The background of transgenic lines were typically from mixed outcrosses of the transgenics to AB, TAB5, and TAB14 strains when regenerating the lines as the working stocks aged. All samples were collected at approximately 120 hpf - natural spawning at 8:30-9:00AM EST on day zero, samples were collected at 8-10AM EST on day 5.

2017-11-12 | GSE104953 | GEO

Transcritomic analysis in untreated and sodium arsenite treated (96-120 hours post fertilization; hpf) in pooled (12-15) zebrafish larval livers 5 days post fertilization (dpf): wild-type TAB5 compared to as3mt mutant larvae

Project description:This study was carried out to compare the changes in gene expression in 5 dpf zebrafish larval livers in response to mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 1 mM sodium arsenite treatment (96-120 hpf)

2023-05-01 | GSE228752 | GEO

Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

Project description:Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

| PRJNA727017 | ENA

Transcriptomic analysis of the liver from control sibling and mutant uhrf1-hi272 zebrafish larvae at 120 hpf treated with DMSO or Palbociclib (PD)

Project description:This study was carried out to compare the changes in gene expression in livers of 120 hpf control sibling and mutant uhrf1-hi272 zebrafish larvae in response to treatment with DMSO or Palbociclib (PD)

2023-07-28 | GSE234993 | GEO

ChIP-chip by array of zebra fish hepatocellular carcinoma and normal liver to detect differences in CG island methylation

Project description:The aim of the experiment was to detect differences in CG island methylation between hepatocellular carcinoma and normal liver in zebrafish. Zebrafish were treated with DMBA, producing hepatocellular carcinoma, genomic DNA was prepared from these and control zebrafish livers. Methylated DNA was immunoprecipitated from HCC and control samples and labeled with Cy5, samples were co-hybridised with Cy3 labeled zebrafish genomic DNA to the Birmingham D. rerio Agilent 025794 45220 v1 microarray.

2011-01-01 | E-MTAB-209 | 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