Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Danio rerio

ABSTRACT: Early life exposure to low levels of AHR agonist 3,3’,4,4’,5-pentachlorobiphenyl (PCB126) reprograms gene expression in adult brain.

PROVIDER: PRJNA386102 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5520630.fastq.gz	Fastqsanger.gz
	SRR5520640.fastq.gz	Fastqsanger.gz
	SRR5520631.fastq.gz	Fastqsanger.gz
	SRR5520641.fastq.gz	Fastqsanger.gz
	SRR5520632.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

PCB126 (3,3',4,4',5-Pentachlorobiphenyl) induced alterations in m6A RNA modifications in zebrafish embryos

Project description:PCB126 (3,3',4,4',5-Pentachlorobiphenyl) induced alterations in m6A RNA modifications in zebrafish embryos

| PRJNA642647 | ENA

Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish (Danio rerio)

Project description:The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). There is extensive knowledge on the range of target genes regulated by AHR ligands. However, there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome-wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours (waterborne exposure) and were reared in clean water for 7 days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing (RRBS) and RNAseq, respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions (DMRs) in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain, PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes (DEGs). We are currently investigating the relationship between DMRs and DEGs.

2017-09-30 | GSE104221 | GEO

Transcription profiling of rat liver after 13 weeks of subchronic exposure to TCDD, PeCDF, PCB126, PCB153 and PCB126/PCB153

Project description:This study investigates the effects of the aryl hydrocarbon receptor (AhR) ligands TCDD, PCB126 and PeCDF; the non-AhR ligand PCB153 and the binary mixture PCB126/PCB153 on hepatic gene expression in female sprague dawley rats. Rats were treated with toxicological equivalent doses of TCDD (100ng/kg), PeCDF (200ng/kg), PCB126 (1000ng/kg) and PCB153 (1000ug/kg) 5 days a week for 13 weeks. Experiment Overall Design: There are 6 control chips and representing animals treated with vehicle control. There are 3 biological replicates (3 chips) for each treatment group (eg. TCDD, PCB126), each biological replicate is derived from 2 individual animals. A total of 21 chips were analyzed. Intensities were normalized using the GC-Robust Multiarray (GCRMA) method through Genetraffic software package.

2008-06-14 | E-GEOD-5789 | biostudies-arrayexpress

Effect of 13 weeks of subchronic exposure to TCDD, PeCDF, PCB126, PCB153 and PCB126/PCB153 on hepatic gene expression

2006-09-08 | GSE5789 | GEO

RNAseq of zebrafish (Danio rerio) developmentally exposed to the polychlorinated biphenyl 3,3'-dichlorobiphenyl (PCB-11)

Project description:3,3’-Dichlorobiphenyl (PCB-11) is a non-legacy PCB congener widely detected in environmental samples and has been detected in human serum, but its toxicity potential is poorly understood. Zebrafish statically exposed to 4,500 µg/L PCB-11 at 24 hours post fertilization (hpf) were collected at 96 hpf for RNA sequencing.

2019-08-22 | GSE118955 | GEO

Danio rerio

Project description:Role of AHR in cardiac developmental toxicity of PAHs

| PRJNA248661 | ENA

Danio rerio

Project description:Next Generation Sequencing (NGS) of zebrafish larvae transcriptome by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment

| PRJNA257195 | ENA

Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site

Project description:This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle. At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation.

2011-06-06 | GSE25245 | GEO

Danio rerio

Project description:PPARγ agonist-induced disruption of dorsoventral patterning in zebrafish

| PRJNA544341 | ENA

Danio rerio

Project description:Next Generation Sequencing (NGS) of zebrafish larvae microRNA expression profilling by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment

| PRJNA335352 | ENA

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