Gene expression profile and molecular pathway datasets resulting from benzo(a)pyrene exposure in the liver and testis of adult tilapia

Benzo(a)pyrene (BaP), the prototype of polycyclic aromatic hydrocarbons, is known to exhibits genotoxic and carcinogenic effects promoting molecular impacts. The dataset presented here is associated with the research article paper entitled “Transcriptome Analysis Reveals Novel Insights Into the Response of Low-dose Benzo(a)pyrene Exposure in Male Tilapia”. In this article, we presented a transcriptomic characterization of male tilapia exposure to BaP in the short term. This data provides an extended analysis of changes in the gene expression and identification of pathways in the liver and testis of male tilapia exposure to BaP. We used gene set enrichment analysis (GSEA) and sub-network enrichment analysis (SNEA) to identify gene networks and pathways associated with molecular adverse effects of BaP exposure. The data indicates that target pathways related to promoting carcinogenesis such as DNA repair and DNA replication were affected as well as other crucial biological processes. Moreover, to determine whether some of the key reported genes of DNA damage are affected by BaP exposure, Quantitative PCR (qPCR) was performed. Gene set categories and sub-networks are provided and the corresponding signature differences from BaP exposure are listed. The information in these datasets may contribute to understanding the potential carcinogenesis mechanism of action from low BaP exposure.

associated with molecular adverse effects of BaP exposure. The data indicates that target pathways related to promoting carcinogenesis such as DNA repair and DNA replication were affected as well as other crucial biological processes. Moreover, to determine whether some of the key reported genes of DNA damage are affected by BaP exposure, Quantitative PCR (qPCR) was performed. Gene set categories and sub-networks are provided and the corresponding signature differences from BaP exposure are listed. The information in these datasets may contribute to understanding the potential carcinogenesis mechanism of action from low BaP exposure.
& 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Specifications table
Subject area Biology More specific subject area Transcriptomics Type of data Table, text file. How data was acquired mRNA data from RNA-Sequencing (RNA-Seq) technology and bioinformatic analysis were used to identify a molecular signature and pathways affected by BaP exposure. Data format Filtered and analyzed.

Experimental factors
Analysis of gene expression profile RNA-Seq data from a BaP experiment Experimental features RNA-Seq reads were trimmed and the clean reads analyzed. Gene read mapping, differential expression analysis (DE) and GSEA and SNEA were performed from tilapia liver and testis tissue after BaP-treatment. Quantitative PCR (qPCR) was used to evaluate the transcriptomic changes observed in BaP-exposed male tilapia. Data source location Sample source and tissue harvest were located at Cinvestav-Merida, Yucatan, Mexico. The BaP experiment was carried out at Cinvestav-Merida. Sample analysis was performed at Cinvestav-Merida and the University of Florida (Gainesville, FL, USA

Value of data
The data explores the biological mechanism of action of BaP in the liver and testis of male tilapia by a high throughput transcriptomic approach (RNA-Sequencing).
The data provides ample information of changes in gene expression, subnetworks and functional enrichment analysis associated with several biological processes after BaP treatment.
The molecular signature identified for BaP exposure is very useful to other researchers that may explore the mechanism of action of BaP in non-model organism such as tilapia.
New gene sets associated with molecular adverse effects of BaP can be useful in understanding the role of BaP into the activation of apoptotic signals in tilapia.
This data may contribute to understanding the BaP mechanisms associated with adverse effects in tilapia.

Data
These data sets provide information on the BaP molecular effects in tilapia testes and liver. Table 1 presents all the primer sets used for qPCR analysis. All primers used were previously validated as indicated in the 2 À ΔΔCT method [2]. Of these genes evaluated, Cyp1b1, Ddit4, Gadd45b and Fasn showed significant changes in their levels of expression from BaP exposure (p o 0.05) ( Table 5 in [1]). Table 2 presents a partial list of the characterization of gene expression profiling of RNA-data by BaP exposure. This data shows a larger number of altered genes in the liver related with adverse molecular effects on the cell cycle and with several other biological processes. Table 3 shows GO categories and Table 4 identifies gene networks altered by a low concentration of BaP in the liver and testis of male tilapia. All significantly altered genes are listed in Table SI as well as identified GO categories and subnetworks which are present.

Experimental design, materials and methods
Liver and testis samples were collected as were controls. Analysis of gene expression profile RNA-Seq was performed as is mentioned in [1]. Briefly, Tilapia RNA-Seq reads were trimmed, clean reads aligned to reference genome using Tophat [3,4]. Differential expression analysis was conducted using exact test with R package EdgeR (p o 0.05; fold change 4 7 1.5 were considered as significant). Elsevier PathwayStudio TM V9 (Elsevier, Inc., Rockville, MD, USA) operating with the ResNet 10.0 database was used to identify the biological mechanism that underlie the BaP effects. The gene set enrichment analysis (GSEA) and subnetwork enrichment analysis (SNEA) algorithms (applying the Mann À Whitney test with an alpha level of p o 0.05) [5][6][7]. Quantitative PCR (qPCR) was used to evaluate the transcriptomic changes of key genes such as Ddit4, Gadd45b and Igf2, Tet3 and Fasn involved in important functions, i.e, DNA damage, growth and development. The rpl8 gene was used as the internal reference normalizer gene.    Table 3 Representative list of GO terms significantly affected in the liver and testis of male tilapia exposed to BaP. Determined by Gene Set Enrichment Analysis (GSEA; p o 0.05, fold change Z 10%).