Validation and bioinformatics analysis of differentially expressed circRNAs involved in developing male Xenopus laevis chronically exposed to atrazine

The data presented here are related to the research article titled “Identification of circular RNAs and their alterations involved in developing male Xenopus laevis chronically exposed to atrazine” (Sai et al., 2018) [1]. Circular RNAs (circRNAs) are implicated in multiple developmental anomalies (Bachmayr-Heyda et al., 2015; Li et al., 2015) [2], [3]. This report describes the differentially expressed circRNAs involved in developing male Xenopus laevis (X. laevis) chronically exposed to atrazine (AZ) database. The database contains the validation of differentially expressed circRNAs, KEGG analysis of differentially expressed circRNA-associated target genes and prediction of miRNA binding sites. These data may help to further evaluate the role of circRNAs in male X. laevis chronically exposed to AZ.


a b s t r a c t
The data presented here are related to the research article titled "Identification of circular RNAs and their alterations involved in developing male Xenopus laevis chronically exposed to atrazine" (Sai et al., 2018) [1]. Circular RNAs (circRNAs) are implicated in multiple developmental anomalies (Bachmayr-Heyda et al., 2015; Li et al., 2015) [2,3]. This report describes the differentially expressed circRNAs involved in developing male Xenopus laevis (X. laevis) chronically exposed to atrazine (AZ) database. The database contains the validation of differentially expressed circRNAs, KEGG analysis of differentially expressed circRNA-associated target genes and prediction of miRNA binding sites. These data may help to further evaluate the role of circRNAs in male X. laevis chronically exposed to AZ Table   Subject area Environmental toxicology More specific subject area CircRNA study involved in developing male Xenopus laevis chronically exposed to 100 µg/L AZ Type of data Table  How data  This is an innovative data, not yet published elsewhere Related research article Identification of circular RNAs and their alterations involved in developing male X. laevis chronically exposed to AZ.
Value of the data 1. The explored data are innovative information.
2. Data represented are unequivocal and innovative research based work. Data would be valuable to the researcher those who are doing research on circRNAs in developing male X. laevis chronically exposed to AZ. 3. Data are valuable for estimating effects of the AZ on male amphibians. 4. Data will help to understand the normal function of circRNAs as well as their roles in response to environmental chemicals like AZ.

Data
The dataset of this article provides information on the differentially expressed circRNAs involved in developing male Xenopus laevis chronically exposed to AZ. Table 1 shows the sequences of primers in the Q-RT-PCR assay for validating the differential expressions of circRNAs involving in developing male X. laevis chronically exposed to 100 µg/L AZ after sequencing. In Table 2, data show the results of Q-RT-PCR validation of the differentially expressed circRNAs. KEGG analysis were performed for the differentially expressed circRNA-associated target genes [4,5]. Table 3 shows the 19 enrichment pathways of differentially expressed circRNAs-associated target genes. MiRNA-binding sites on cir-cRNAs predicted by custom-written software based on Targetscan and Miranda software (Cloud-Seq Biotech Ltd. Co., Shanghai, China). From the data (Table 4), it can be seen that 282 circRNAs linked to X. laevis exposed to 100 µg/L AZ for 180 days had predicted miRNA targets by custom-written software.

Validation of differentially expressed circRNAs
We validated the expression of circRNAs identified by RNA-seq using Quantitative RT-PCR (Q-RT-PCR,ViiA 7 Real-time PCR System, Applied Biosystems, Carlsbad, CA, USA) for which we selected 8 circRNAs with the divergent primers as listed in Table 1. The circRNAs were chosen based on their functional roles and respective FC values. For Q-RT-PCR analysis, total RNA was converted into cDNA using the Invitrogen Superscript cDNA Synthesis kit (Invitrogen Corp., Carlsbad, CA, USA). Reactions were performed according to the manufacturer's instructions. Relative circRNAs expression was Table 1 Sequences of primers in the Q-RT-PCR assay for validating the differential expressions of circRNAs after sequencing.  [6]. The upregulated circRNAs were identified at 2-△△CT 41, the downregulated circRNAs were identified at 2-△△CTo 1. The expression of gene gpi.S (NM_001092296.1) was used as a reference for data normalization, because it was reported to be a housekeeping gene [7]. The Q-RT-PCR assays were performed in three replicates. Statistical analysis was conducted using the SPSS Statistics 18.0 software (IBM Corp., New York, NY, USA). Significant difference between control and AZ-treated groups was compared using student's t-test at p o 0.05.

Bioinformatic analysis
KEGG analysis were performed for the differentially expressed circRNA-associated target genes [5,8]. MiRNA-binding sites on circRNAs are all predicted by custom-written software based on Targetscan and Miranda software (Cloud-Seq Biotech Ltd. Co., Shanghai, China). Sequences of the primers used were listed in Table 1. Table 3 The enrichment pathways of differentially expressed circRNAs-associated target genes by KEGG.  Table 4 The top 5 predicted miRNA targets for 282 circRNAs linked to X. laevis exposed to 100 µg/L AZ for 180 days.