Whole transcriptome data of zebrafish exposed to chronic dose of depleted uranium

The concentration of depleted uranium (DU) in the environment is expected to increase due to anthropogenic activities, posing potential risks on ecosystems. The effects of chronic exposure to DU at concentration close to the environmental standards (0.3–30 µg DU/L) are scarcely characterised. Genomic alterations caused by low doses of pollutants can potentially propagate over generations, but how these effects may affect the health of the progeny remain uncertain for the vast majority of toxicants. The present dataset describes the transcriptomic effects of a chronic exposure to 20 µg DU/L during 10 days on adult zebrafish (Danio rerio) organs, the brain, the testis and the ovaries. The potential multigenerational effects of DU were assessed on the progeny of the adult exposed fish at the two-cells stage and after four days of development. We describe in this article the summary statistics of the differential gene expression analysis and focus on key molecular pathways affected by an exposure to a low concentration of DU. The data presented in this study supports the observation made in Armant et al. (2017) [1] (https://doi.org/10.1016/j.dib.2016.05.007) that DU can induce a molecular stress in both adult zebrafish and their progeny. The raw dataset has been deposited at the Gene Expression Omnibus (GEO) repository under the accession number GEO:GSE96603.


a b s t r a c t
The concentration of depleted uranium (DU) in the environment is expected to increase due to anthropogenic activities, posing potential risks on ecosystems. The effects of chronic exposure to DU at concentration close to the environmental standards (0.3-30 µg DU/L) are scarcely characterised. Genomic alterations caused by low doses of pollutants can potentially propagate over generations, but how these effects may affect the health of the progeny remain uncertain for the vast majority of toxicants. The present dataset describes the transcriptomic effects of a chronic exposure to 20 µg DU/L during 10 days on adult zebrafish (Danio rerio) organs, the brain, the testis and the ovaries. The potential multigenerational effects of DU were assessed on the progeny of the adult exposed fish at the two-cells stage and after four days of development. We describe in this article the summary statistics of the differential gene expression analysis and focus on key molecular pathways affected by an exposure to a low concentration of DU. The data presented in this study supports the observation made in Armant   Wild type versus exposed to depleted uranium

Experimental features
Comparison of the transcriptomic response from adult zebrafish tissues (brain, ovaries and testis) exposed to depleted uranium and their progeny (at two times of development) to their respective controls.

Value of the data
Depleted uranium is a heavy metal posing potential environmental risks due to its increasing release from anthropogenic activities.
This dataset presents the differentially expressed genes in adult brain and gonads (testis and ovaries) from zebrafish exposed to 20 µg/L depleted uranium for 10 days.
It also provides the potential multigenerational effects of a parental exposure to depleted uranium in the progeny of exposed fish at both the two-cells stage and on four-days larvae.
The analysis of the biological pathways impacted by a chronic depleted uranium exposure will help to understand the molecular mechanisms of toxicity of this toxicant or other heavy metals.
The identification of the depleted uranium (DU) de-regulated genes could lead to the development of biomarkers of DU and other heavy metals.

Data
This data consists of 35 high-throughput sequencing samples of adult brain, testis and ovaries obtained from adult zebrafish exposed to 20 µg/L of depleted uranium (DU) for 10 days, as well as their progeny both at the two-cells stage and four-days larvae (96 h post-fertilization, hpf) [1,2]. The data are deposited under the Gene Expression Omnibus (GEO) number GEO: GSE96603 at http:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc ¼ GSE96603. The list of samples collected in this study is provided in Table 1. The principal component analysis on the regularized log transformed (rlog) expression data shows at the global level that the biological replicates group by stage and tissue (Fig. 1). A selection of 22 samples with low biological variability was made for the differential expression analysis ( Table 2, Fig. 1B). The summary statistics of the deregulated genes obtained after pairwise differential analysis is provided in Table 3. The expression of a selection of genes involved in diverse biological processes (such as cell adhesion, response to oxidative stress, ATPase activity, protein chaperons, lipid metabolism, hatching and tissue regeneration) altered after DU-exposure is displayed in Fig. 2. The gene ontology analysis (GO) was applied to classify the most significantly affected pathways in each condition (Table 4).    Table 2 List of the 22 samples with the lowest biological variabilities.

C2cells_r1 2 cells embryos
Progeny of adult exposed fish C2cells_r2 2 cells embryos Progeny of adult exposed fish C2cells_r4 2 cells embryos Progeny of adult exposed fish C96hpf_l2 96 hpf larvae Progeny of adult exposed fish C96hpf_l3 96 hpf larvae Progeny of adult exposed fish CbrainF_b2 Adult brain 20 µg/L depleted uranium CbrainF_b5 Adult brain 20 µg/L depleted uranium CovaryF_g1 Adult ovary 20 µg/L depleted uranium CovaryF_g2 Adult ovary 20 µg/L depleted uranium CtestesM_g3 Adult testis 20 µg/L depleted uranium CtestesM_g5 Adult testis 20 µg/L depleted uranium U2cells_r1 2 cells embryos Progeny of adult exposed fish U2cells_r3 2 cells embryos Progeny of adult exposed fish U2cells_r5 2 cells embryos Progeny of adult exposed fish U96hpf_l2 96 hpf larvae Progeny of adult exposed fish U96hpf_l3 96 hpf larvae Progeny of adult exposed fish UbrainF_b2 Adult brain 20 µg/L depleted uranium UbrainF_b5 Adult brain 20 µg/L depleted uranium UovaryF_g1 Adult ovary 20 µg/L depleted uranium UovaryF_g4 Adult ovary 20 µg/L depleted uranium UtestesM_g3 Adult testis 20 µg/L depleted uranium UtestesM_g5 Adult testis 20 µg/L depleted uranium the mating for 4 more days (10 days in total). Embryos were grown in clean water for 4 days at 28°C in incubators (TC series, Aqualytics). No death, behavioural differences or sign of suffering were observed in the DU-exposed fish group as compared to controls. Measurement of body mass and length didn't reveal any difference between the exposed and control group. All fish were killed by immersion in ice cold water at the end of the experiment and tissue dissected under the binocular (Leica, France).

Extraction of total RNA
Total RNA was extracted with the Absolutely RNA Miniprep kit (Agilent) according to manufacturer's recommendations. Single adult tissue was used for the extraction. Pools of three larvae were used at the four-days stage and pools of 50 embryos at two-cells stage. RNA integrity was checked by loading about 100 ng total RNA on a RNA6000 Nanochip using an Agilent 2100 Bioanalyser (Agilent Technologies). Samples showed no sign of degradation (RNA index number 48).

Library preparation, quality control
Total RNA (1 µg) was subjected to two rounds of poly(A) RNA selection using poly-dT coated magnetic beads using the strand-oriented TruSeq mRNA kit v2 (Illumina) following manufacturer's protocol. First-strand cDNA synthesis was performed with the Superscript II (Thermo Fisher) using random hexamer primers, cDNA fragments subjected to end-repair, dA-tailing, and finally ligated to adapters. Libraries were amplified by 12 cycles of PCR. The quality and concentration of the Heatmap of a selection of differentially expressed genes. A. Significant FDR from each comparative analysis are displayed in yellow (depleted uranium versus control), and non-significant FDR in black. Absent FDR were set to 1 (non-significant) and FDRo 10 −6 fitted to 10 −6 . B. Fold changes obtained from the differential gene expression analysis: down-regulated genes in blue, no change in expression in white, up-regulated genes in red.

Table 4
Gene ontology analysis. The list provides the top 5 biological pathways impacted by DU in each dataset based on smallest pvalues.

Set of genes
Gene ontology term p-value Down in DU exposed brain . Bad quality reads were filtered out with trimgalore using the option -q 30 and -paired.

Data analysis
Mapping of filtered reads was performed on the Zv10 indexed genome generated with the exonexon information from Ensembl (release 85) with RNA-STAR [3] using the options -alignIntronMax 1000000 -alignMatesGapMax 1000000 -alignIntronMin 20 -outFilterMultimapNmax 20 -out-WigStrand Stranded -quantMode TranscriptomeSAM GeneCounts. Quantification and normalization of the mapped reads at the level of gene model were performed with DESeq. 2 [4]. Adjusted p-values (False Discovery Rate, FDR) o 0.01 and fold-change 4 ¼ 72 were used to detect significant differential gene expression. Gene Ontology (GO) analysis was performed with the R package TopGO using the Danio rerio annotations from Ensembl (release 85).

Ethic approval
All experiments were made in accordance with the French animal protection standards and were approved by the Animal User and Ethical Committee at the IRSN (committee 81).