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RNA seq data examining response to chemical treatment to build the first gene co-expression network of zebrafish

ABSTRACT: RNA seq data examining response to chemical treatment to build the first gene co-expression network of zebrafish

PROVIDER: PRJNA721440 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14217600.fastq.gz	Fastqsanger.gz
	SRR14217700.fastq.gz	Fastqsanger.gz
	SRR14217601.fastq.gz	Fastqsanger.gz
	SRR14217701.fastq.gz	Fastqsanger.gz
	SRR14217602.fastq.gz	Fastqsanger.gz

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RNA seq data examining response to chemical treatment to build the first gene co-expression network of zebrafish

Project description:This study combines RNA seq data from a number of different expeirments examining response to chemical treatment to build the first gene co-expression network of zebrafish. We interrogate this network to determine how the transcriptomic map responds to different types of chemicals and what pathways and processes are critical to chemical response

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Project description:BackgroundZebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify genes and biological pathways that Aryl Hydrocarbon Receptor 2 (AHR2) Activators and flame retardant chemicals (FRCs) alter in developing zebrafish. Taking advantage of a compendium of phenotypically-anchored RNA sequencing data collected from 48-h post fertilization (hpf) zebrafish, we inferred a co-expression network that grouped genes based on their transcriptional response.ResultsGenes responding to the FRCs and AHR2 Activators localized to distinct regions of the network, with FRCs inducing a broader response related to neurobehavior. AHR2 Activators centered in one region related to chemical stress responses. We also discovered several highly co-expressed genes in this module, including cyp1a, and we subsequently show that these genes are definitively within the AHR2 signaling pathway. Systematic removal of the two chemical types from the data, and analysis of network changes identified neurogenesis associated with FRCs, and regulation of vascular development associated with both chemical classes. We also identified highly connected genes responding specifically to each class that are potential biomarkers of exposure.ConclusionsOverall, we created the first zebrafish chemical-specific gene co-expression network illuminating how chemicals alter the transcriptome relative to each other. In addition to our conclusions regarding FRCs and AHR2 Activators, our network can be leveraged by other studies investigating chemical mechanisms of toxicity.

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