Literature DB >> 29900306

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

Linlin Sai1, Ling Li1, Chenyang Hu1, Binpeng Qu2, Qiming Guo1, Qiang Jia1, Yu Zhang1, Cunxiang Bo1, Xiangxin Li3, Hua Shao1, Jack C Ng4, Cheng Peng1,4.   

Abstract

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.

Entities:  

Keywords:  CircRNA; CircRNA-miRNA; Herbicide; KEGG; Q-RT-PCR; Reproductive toxicology

Year:  2018        PMID： 29900306      PMCID： PMC5996731          DOI： 10.1016/j.dib.2018.04.011

Source DB:  PubMed          Journal:  Data Brief        ISSN： 2352-3409


Specifications Table Value of the data The explored data are innovative information. 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. Data are valuable for estimating effects of the AZ on male amphibians. 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 circRNAs 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.
Table 1

Sequences of primers in the Q-RT-PCR assay for validating the differential expressions of circRNAs after sequencing.

Target namePrimer nameSequence (5′→3′)Product length
NC_030732.1:43721272–43728946-1-ForwardGGCTATGGTAACCGTGGAAA186
1-ReverseTTTTCACACCCCGTTTCTTC









NC_030734.1:102788414–102788574-2-ForwardAGCAAGAAATGTTGCTGGAGA136
2-ReverseGTCCCTGTCCCTGAGAGGTT









NC_030734.1:106398702–106449286+3-ForwardCCTGTTGCTTAGGCCATCAT213
3-ReverseTGTGATGAGGCAGAGTTTCG









NC_030734.1:14617230–14633443-4-ForwardCTAACACCACCCTCGTCCAT193
4-ReverseTCATTCTGGTCAAGGGCTTT









NC_030735.1:109227383–109290634-5-ForwardACTGCAGGCATCTCTTGGAC200
5-ReverseGCCAAAAACAACTGCCAAAT









NC_030737.1:31865134–31952348-6-ForwardCATTTTGCATTGGCATGTTT188
6-ReverseATCGCACAAAGTCCCATCTC









NC_030738.1:39776310–39778799-7-ForwardTCAGAATGCAGCTGTCAAGG199
7-ReverseCTGGATTTCCACCATCCTCA









NC_030740.1:57091911–57092116+8-ForwardGGCTACCAGAATCGTCATGC197
8-ReverseATGCTGTTGCTGATTGGATG









NW_016694872.1:550852-632532-9-ForwardCTTCTGTGGTCACCGGAAGT189
9-ReverseTGGACATGTGAACTGGGTGT









NC_030738.1:21126033–21131815+10-ForwardCCATGCATTCCACTAGGTCA191
10-ReverseATCACTCACTGACGCACGAG









NM_001092296.111-ForwardGAGGACCTCGTGTGTGGTTT60
11-ReverseCCAGAGTTTTGGCAATGTGA
Table 2

The results of Q-RT-PCR validation of the differentially expressed circRNAs.

Differentially expressed circRNAs2-△△ CTP-value
NC_030732.1:43721272–43728946-0.5190.037
NC_030734.1:102788414–102788574-0.4570.046
NC_030734.1:106398702–106449286+0.5610.049
NC_030735.1:109227383–109290634-0.4900.047
NC_030737.1:31865134–31952348-0.8020.014
NC_030738.1:39776310–39778799-2.4800.040
NW_016694872.1:550852-632532-0.4720.045
NC_030738.1:21126033–21131815+10.5120.036

Sequences of the primers used were listed in Table 1.

Table 3

The enrichment pathways of differentially expressed circRNAs-associated target genes by KEGG.

PathwayIDDefinitionFisher-PvalueCountFDREnrichment ScoreGene Ratio
xla04310Wnt signaling pathway0.0006251532730.087565593.2040140.06
xla04510Focal adhesion0.001048693680.087565592.9793530.0725
xla04114Oocyte meiosis0.0017986771960.10012632.7450470.045
xla04010MAPK signaling pathway0.0030757894680.12841422.5120440.0825
xla04622RIG-I-like receptor signaling pathway0.0051226651200.15236132.2905040.03
xla04115p53 signaling pathway0.0054740591210.15236132.2616910.03
xla04012ErbB signaling pathway0.0064776621550.15453852.1885820.035
xla04340Hedgehog signaling pathway0.007444835810.15541092.1281450.0225
xla04920Adipocytokine signaling pathway0.010744671320.19937331.9688070.03
xla00480Glutathione metabolism0.01256994880.20391341.9006670.0225
xla04912GnRH signaling pathway0.013431421860.20391341.8718780.0375
xla00515Mannose type O-glycan biosynthesis0.01902007500.25453461.7207880.015
xla04914Progesterone-mediated oocyte maturation0.02129951620.25453461.6716310.0325
xla04146Peroxisome0.023165561300.25453461.6351570.0275
xla00601Glycosphingolipid biosynthesis - lacto and neolacto series0.02344076820.25453461.6300280.02
xla04144Endocytosis0.024386555020.25453461.612850.0775
xla04068FoxO signaling pathway0.028779942590.28272061.540910.045
xla04810Regulation of actin cytoskeleton0.039340013840.36498791.4051650.06
xla00533Glycosaminoglycan biosynthesis - keratan sulfate0.04531492460.39829431.3437590.0125
Table 4

The top 5 predicted miRNA targets for 282 circRNAs linked to X. laevis exposed to 100 µg/L AZ for 180 days.

circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030728.1:107931245–107932206+xla-miR-133dxla-miR-133axla-miR-133b
NC_030740.1:64855970–64877155+xla-miR-18xla-miR-19b
NC_030741.1:10475414–10475723+xla-miR-18
NC_030726.1:160156875–160159679-xla-miR-205
NC_030734.1:106485869–106486720-xla-miR-427xla-miR-133dxla-miR-133bxla-miR-133a
NC_030726.1:76691651–76698216+xla-miR-15cxla-miR-429xla-miR-194xla-miR-703xla-miR-23a
NC_030724.1:25016701–25021875+xla-miR-427xla-miR-363xla-miR-223xla-miR-133axla-miR-133b
NC_030726.1:102820197–102823698-xla-miR-92axla-miR-133axla-miR-133dxla-miR-133b
NC_030736.1:12689783–12690847-xla-miR-19b
NC_030727.1:94629493–94639781+xla-miR-15cxla-miR-19bxla-miR-20xla-miR-18xla-miR-429
NC_030737.1:50553238–50553849-xla-miR-427xla-miR-428
NC_030726.1:154989366–154998753+xla-miR-703xla-miR-427xla-miR-205
NC_030733.1:34483227–34511810-xla-miR-15cxla-miR-20xla-miR-19bxla-miR-1bxla-miR-18
NC_030732.1:108698546–108701014-xla-miR-23axla-miR-92a
NC_030741.1:23757079–23761365+xla-miR-223
NW_016694888.1:355851-357777+xla-miR-24bxla-miR-1bxla-miR-194xla-miR-429xla-miR-18
NC_030725.1:145886684–145893268-xla-miR-427xla-miR-363xla-miR-428xla-miR-23a
NC_030725.1:160273437–160274678+xla-miR-429
NC_030736.1:93771653–93772342+xla-miR-427xla-miR-18xla-miR-703xla-miR-428
NC_030725.1:33745008–33747282-xla-miR-19bxla-miR-223xla-miR-194xla-miR-24bxla-miR-1b
NC_030736.1:95594264–95594855+xla-miR-428xla-miR-427xla-miR-20
NC_030729.1:59204043–59212585+xla-miR-205xla-miR-15cxla-miR-1306
NW_016694811.1:4160983-4163596-xla-miR-15cxla-miR-92a
NC_030725.1:75897770–75940162-xla-miR-15c
NC_030732.1:53423582–53432267+xla-miR-19bxla-miR-15cxla-miR-703
NC_030734.1:85835741–85846351-xla-miR-20xla-miR-133dxla-miR-427xla-miR-142xla-miR-15c
NC_030732.1:43721272–43728946-xla-miR-19bxla-miR-205xla-miR-133dxla-miR-133bxla-miR-133a
NC_030732.1:22358736–22365805-xla-miR-205xla-miR-363xla-miR-18xla-miR-19b
NC_030741.1:63398525–63424921-xla-miR-429
NC_030726.1:153762674–153762866-xla-miR-20xla-miR-427xla-miR-428
NC_030727.1:94976453–94990031-xla-miR-142
NC_030740.1:14329209–14332656+xla-miR-15cxla-miR-24b
NC_030726.1:68684168–68687145+xla-miR-19b
NC_030728.1:62905308–62912700-xla-miR-15c
NC_030735.1:109227383–109290634-xla-miR-18xla-miR-15cxla-miR-427xla-miR-20xla-miR-223
NC_030737.1:80523685–80526513+xla-miR-429
NC_030734.1:94791370–94802295-xla-miR-142
NC_030731.1:70450630–70453977-xla-miR-15cxla-miR-1b
NW_016694850.1:165938-168684-xla-miR-19bxla-miR-23axla-miR-24b
NC_030724.1:162927448–162932292+xla-miR-205xla-miR-23axla-miR-703
circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030726.1:170141772–170152857+xla-miR-19bxla-miR-363xla-miR-133dxla-miR-133bxla-miR-133a
NC_030724.1:20602441–20604471-xla-miR-205
NC_030732.1:93793150–93820672+xla-miR-1b
NC_030728.1:130780434–130781838-xla-miR-23axla-miR-19b
NC_030730.1:87897066–87916110-xla-miR-427
NC_030724.1:16657286–16660198+xla-miR-15cxla-miR-1306
NC_030737.1:38242321–38257632+xla-miR-23axla-miR-142
NC_030731.1:109099315–109104730-xla-miR-19bxla-miR-223xla-miR-427xla-miR-1bxla-miR-20
NC_030725.1:12393643–12395967-xla-miR-23a
NC_030726.1:27655736–27658064+xla-miR-223xla-miR-1b
NC_030727.1:67838131–67839236-xla-miR-223xla-miR-18
NC_030740.1:78837348–78837807-xla-miR-1b
NC_030739.1:3829594–3830014+xla-miR-205xla-miR-19b
NC_030724.1:174501216–174522171+xla-miR-19b
NC_030725.1:115717672–115718776-xla-miR-18xla-miR-20xla-miR-429xla-miR-133dxla-miR-1b
NC_030734.1:41157487–41160006+xla-miR-205xla-miR-20
NC_030732.1:19072979–19073580-xla-miR-428xla-miR-427
NC_030734.1:109280643–109285081-xla-miR-194
NC_030733.1:50631948–50642076-xla-miR-427xla-miR-428xla-miR-703
NC_030726.1:130247524–130272922+xla-miR-15cxla-miR-194
NC_030731.1:80596587–80599136-xla-miR-142xla-miR-23axla-miR-427xla-miR-20xla-miR-428
NC_030739.1:36191184–36191805+xla-miR-20xla-miR-19b
NC_030725.1:11616097–11616889+xla-miR-1306
NC_030727.1:128265094–128266804+xla-miR-427xla-miR-24bxla-miR-703
NC_030740.1:105999689–106002961-xla-miR-19b
NC_030733.1:23052893–23053431+xla-miR-703
NC_030730.1:70393563–70405777+xla-miR-20xla-miR-1bxla-miR-142xla-miR-428xla-miR-223
NC_030737.1:83574596–83583489+xla-miR-15cxla-miR-427xla-miR-428xla-miR-194xla-miR-18
NC_030727.1:66053235–66057876-xla-miR-1bxla-miR-20xla-miR-428xla-miR-427
NC_030728.1:62937674–62947488+xla-miR-703xla-miR-18
NC_030738.1:68976380–68977086-xla-miR-18xla-miR-427
NW_016694892.1:26153-27290+xla-miR-363
NC_030724.1:143151804–143152935-xla-miR-18
NC_030734.1:98881558–98914095-xla-miR-23axla-miR-19b
NC_030734.1:57200126–57207190+xla-miR-1b
NC_030732.1:62658175–62664193+xla-miR-205xla-miR-429
NC_030729.1:59341935–59363703-xla-miR-427xla-miR-18xla-miR-15cxla-miR-703xla-miR-429
NC_030740.1:66890501–66890846+xla-miR-142xla-miR-15c
NC_030738.1:55306347–55307113+xla-miR-20xla-miR-363
NC_030732.1:49586121–49588850-xla-miR-205xla-miR-19b
NC_030741.1:101502504–101503105+xla-miR-15c
NW_016694865.1:628498-632223+xla-miR-23a
circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030724.1:35396202–35400617+xla-miR-23a
NC_030733.1:6201642–6201910+xla-miR-223xla-miR-24bxla-miR-205
NC_030735.1:17768662–17785569+xla-miR-23a
NC_030727.1:132699431–132699787-xla-miR-15cxla-miR-428
NC_030724.1:105611901–105637401+xla-miR-15cxla-miR-142xla-miR-427xla-miR-223xla-miR-18
NC_030729.1:64339785–64361328+xla-miR-427xla-miR-133axla-miR-133dxla-miR-133bxla-miR-15c
NC_030737.1:32708865–32717748-xla-miR-428xla-miR-20
NC_030732.1:65055266–65057014-xla-miR-15c
NC_030735.1:95974107–95989476-xla-miR-92axla-miR-703xla-miR-1bxla-miR-205
NC_030727.1:77776018–77777622+xla-miR-19bxla-miR-20xla-miR-142xla-miR-427
NC_030738.1:1661483–1662700-xla-miR-19bxla-miR-15cxla-miR-133axla-miR-133dxla-miR-133b
NC_030728.1:123007127–123007546-xla-miR-703
NC_030739.1:7513676–7514449-xla-miR-133dxla-miR-133bxla-miR-133a
NC_030740.1:75628520–75629574-xla-miR-1bxla-miR-429xla-miR-428xla-miR-427xla-miR-23a
NC_030732.1:74604196–74606604+xla-miR-19bxla-miR-15cxla-miR-142xla-miR-194xla-miR-133d
NC_030730.1:10150206–10153200+xla-miR-18
NC_030735.1:8450716–8468533-xla-miR-20xla-miR-142
NC_030729.1:70852510–70871306+xla-miR-142
NC_030732.1:1244473–1252348+xla-miR-429xla-miR-18xla-miR-703xla-miR-15cxla-miR-142
NC_030728.1:107378386–107381277+xla-miR-23axla-miR-133axla-miR-703
NC_030724.1:179432037–179435517-xla-miR-18xla-miR-1b
NC_030734.1:106398702–106449286+xla-miR-18xla-miR-20xla-miR-142xla-miR-223xla-miR-15c
NC_030729.1:64054605–64065892-xla-miR-20xla-miR-428xla-miR-15cxla-miR-223xla-miR-92a
NC_030724.1:170644099–170649196+xla-miR-427xla-miR-428xla-miR-205xla-miR-19b
NC_030729.1:37773578–37779829-xla-miR-24b
NC_030731.1:51165922–51175381-xla-miR-1306
NC_030724.1:175775086–175790852+xla-miR-133dxla-miR-133bxla-miR-133axla-miR-19bxla-miR-23a
NC_030728.1:90621739–90639104+xla-miR-133dxla-miR-133bxla-miR-133axla-miR-20xla-miR-18
NC_030734.1:74355300–74391682-xla-miR-427xla-miR-19bxla-miR-15c
NC_030741.1:25327114–25329691-xla-miR-223xla-miR-1bxla-miR-20
NC_030735.1:35939491–35949048+xla-miR-15cxla-miR-429xla-miR-19b
NC_030730.1:112956827–112961455+xla-miR-20xla-miR-18xla-miR-427xla-miR-92axla-miR-23a
NW_016694899.1:44366-53978+xla-miR-205
NC_030728.1:76506768–76582180+xla-miR-428xla-miR-427xla-miR-223xla-miR-1b
NC_030738.1:15457803–15459103+xla-miR-1b
NC_030739.1:94955628–94960533-xla-miR-20xla-miR-15cxla-miR-18
NC_030733.1:135562111–135567376+xla-miR-1306
NC_030736.1:34659166–34659570+xla-miR-24b
NC_030734.1:64782892–64788817-xla-miR-427xla-miR-428xla-miR-223
NC_030734.1:120248478–120250470+xla-miR-18
NC_030738.1:39776310–39778799-xla-miR-1bxla-miR-194xla-miR-223xla-miR-133axla-miR-133d
circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030730.1:51360379–51374736+xla-miR-427xla-miR-18xla-miR-24bxla-miR-15cxla-miR-428
NC_030740.1:46992144–46992645-xla-miR-1306xla-miR-1b
NC_030725.1:11611649–11617677+xla-miR-15cxla-miR-1bxla-miR-18xla-miR-428xla-miR-20
NC_030724.1:43830404–43835537+xla-miR-15cxla-miR-1b
NC_030738.1:74755329–74775455+xla-miR-205xla-miR-429xla-miR-15cxla-miR-20xla-miR-428
NC_030729.1:56464730–56475693-xla-miR-428xla-miR-427
NC_030738.1:84049851–84051635-xla-miR-15cxla-miR-703xla-miR-19bxla-miR-23a
NC_030736.1:16180713–16182409-xla-miR-20
NC_030724.1:211185447–211186783-xla-miR-1306xla-miR-18
NC_030734.1:51792811–51831507-xla-miR-18xla-miR-429xla-miR-15c
NC_030734.1:57246068–57252093+xla-miR-703
NC_030738.1:88279403–88282053-xla-miR-427xla-miR-24b
NC_030728.1:61473030–61481424-xla-miR-20
NW_016694908.1:92927-96080-xla-miR-427xla-miR-428xla-miR-15c
NC_030734.1:50722600–50728393+xla-miR-92axla-miR-428xla-miR-427xla-miR-223
NC_030733.1:17916295–17924623+xla-miR-24b
NC_030736.1:79090419–79101144+xla-miR-20xla-miR-427xla-miR-428xla-miR-18
NC_030736.1:56496358–56501284+xla-miR-15cxla-miR-133dxla-miR-133axla-miR-133b
NC_030727.1:121417610–121420694+xla-miR-205
NC_030741.1:26301283–26301893-xla-miR-427xla-miR-23a
NC_030735.1:32206764–32213523+xla-miR-205
NC_030739.1:77943686–77949468-xla-miR-20xla-miR-24b
NC_030737.1:75371414–75374264+xla-miR-427xla-miR-428xla-miR-194xla-miR-18
NC_030735.1:14601186–14607078-xla-miR-223xla-miR-15c
NC_030739.1:70343848–70346398+xla-miR-1bxla-miR-18
NC_030726.1:85184232–85191077+xla-miR-23a
NC_030738.1:79443529–79452085-xla-miR-429xla-miR-703xla-miR-18xla-miR-19bxla-miR-223
NC_030735.1:20207460–20231569-xla-miR-133dxla-miR-133axla-miR-133bxla-miR-1bxla-miR-92a
NC_030741.1:98450239–98451611-xla-miR-205
NC_030729.1:21099855–21102101+xla-miR-1bxla-miR-429
NC_030733.1:106477757–106479687+xla-miR-205
NC_030740.1:44305313–44305491-xla-miR-427xla-miR-20xla-miR-428
NC_030726.1:177942280–177943562-xla-miR-427
NC_030727.1:7116105–7120556+xla-miR-427xla-miR-19bxla-miR-223xla-miR-205xla-miR-428
NC_030726.1:54224212–54254306-xla-miR-20xla-miR-92axla-miR-15cxla-miR-363xla-miR-427
NC_030739.1:83804071–83806502-xla-miR-427xla-miR-428
NC_030734.1:48548571–48568404-xla-miR-205xla-miR-15cxla-miR-1bxla-miR-194
NC_030740.1:2067198–2069340-xla-miR-205
NC_030725.1:8987622–8997647+xla-miR-429xla-miR-1306
NC_030734.1:125970779–125973748+xla-miR-24bxla-miR-15c
NC_030735.1:58608320–58651287-xla-miR-429xla-miR-92axla-miR-1b
circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030740.1:80604396–80624781+xla-miR-92axla-miR-1bxla-miR-142
NW_016694822.1:2716268-2716475-xla-miR-19bxla-miR-133dxla-miR-133axla-miR-133b
NC_030738.1:38290681–38293041-xla-miR-133axla-miR-223xla-miR-133dxla-miR-133bxla-miR-142
NC_030731.1:52030005–52047024+xla-miR-427xla-miR-428xla-miR-20xla-miR-205xla-miR-1b
NC_030725.1:117438012–117441967+xla-miR-427xla-miR-1bxla-miR-15cxla-miR-428xla-miR-223
NC_030740.1:73055418–73056718+xla-miR-24bxla-miR-205
NC_030737.1:31865134–31952348-xla-miR-20xla-miR-142xla-miR-427xla-miR-18xla-miR-15c
NC_030732.1:17917996–17922482+xla-miR-703
NC_030737.1:47620341–47648895-xla-miR-20xla-miR-205
NC_030733.1:39169680–39175656+xla-miR-205
NC_030724.1:104426383–104459491+xla-miR-194xla-miR-1b
NC_030728.1:103186982–103187819+xla-miR-142xla-miR-20
NC_030734.1:14617230–14633443-xla-miR-427xla-miR-363
NC_030729.1:52242029–52243410-xla-miR-427xla-miR-20
NW_016694810.1:2911866-2917505-xla-miR-20xla-miR-427xla-miR-428xla-miR-15cxla-miR-18
NC_030726.1:29799927–29804271+xla-miR-363xla-miR-223xla-miR-205
NC_030733.1:68560883–68632668-xla-miR-18xla-miR-20xla-miR-363xla-miR-15cxla-miR-427
NC_030733.1:35161214–35169222-xla-miR-429
NC_030726.1:137849524–137865898-xla-miR-15cxla-miR-92axla-miR-23a
NC_030726.1:120212181–120225907-xla-miR-15cxla-miR-1b
NC_030727.1:108870339–108903815+xla-miR-429xla-miR-23axla-miR-24bxla-miR-703xla-miR-19b
NC_030727.1:90727016–90750200+xla-miR-428xla-miR-427xla-miR-194xla-miR-20xla-miR-15c
NC_030739.1:78251616–78253656+xla-miR-133dxla-miR-133axla-miR-133b
NC_030740.1:26168837–26175753+xla-miR-23a
NC_030736.1:71193885–71201216+xla-miR-427xla-miR-20xla-miR-428xla-miR-205xla-miR-23a
NC_030729.1:47521021–47526563+xla-miR-427xla-miR-428
NC_030734.1:102704770–102705434+xla-miR-427xla-miR-23axla-miR-428
NC_030734.1:19406998–19413599+xla-miR-19bxla-miR-223xla-miR-15cxla-miR-703
NW_016694872.1:550852-632532-xla-miR-18xla-miR-363xla-miR-20xla-miR-1bxla-miR-15c
NC_030731.1:77335237–77338872-xla-miR-24b
NC_030725.1:146024662–146027824+xla-miR-429xla-miR-133dxla-miR-133bxla-miR-133a
NC_030730.1:67190695–67207690+xla-miR-15cxla-miR-703
NC_030736.1:36038622–36040030+xla-miR-363
NC_030739.1:5643839–5666538+xla-miR-205xla-miR-18xla-miR-24b
NC_030732.1:108516037–108521820+xla-miR-429xla-miR-18xla-miR-23a
NC_030729.1:75130409–75139259-xla-miR-223xla-miR-1bxla-miR-429xla-miR-23axla-miR-205
NC_030724.1:132183425–132186548+xla-miR-15cxla-miR-427xla-miR-428
NC_030739.1:97616880–97621201+xla-miR-427
NC_030726.1:162054139–162061530-xla-miR-133axla-miR-133bxla-miR-133dxla-miR-19b
NC_030730.1:15778582–15786224+xla-miR-23axla-miR-133dxla-miR-133bxla-miR-133axla-miR-363
NC_030735.1:52049437–52059905-xla-miR-15cxla-miR-142
circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030725.1:109818399–109821042-xla-miR-23a
NC_030725.1:97240333–97250262+xla-miR-133dxla-miR-133axla-miR-133b
NC_030724.1:156827563–156854793-xla-miR-205xla-miR-92axla-miR-15c
NC_030728.1:130323191–130324520-xla-miR-24bxla-miR-194
NC_030731.1:115219575–115229231+xla-miR-15cxla-miR-194xla-miR-18xla-miR-703xla-miR-23a
NC_030741.1:76210374–76210613-xla-miR-18xla-miR-15c
NC_030727.1:107177485–107182142-xla-miR-363
NC_030728.1:95458531–95464536+xla-miR-23axla-miR-133axla-miR-133dxla-miR-133bxla-miR-429
NC_030737.1:72301049–72303697+xla-miR-363
NC_030733.1:108871513–108873513-xla-miR-15c
NC_030740.1:26948790–26979571+xla-miR-15cxla-miR-194
NC_030738.1:21126033–21131815+xla-miR-19bxla-miR-133dxla-miR-133axla-miR-18xla-miR-363
NC_030737.1:4840276–4844107-xla-miR-703xla-miR-15c
NC_030730.1:86419246–86419592-xla-miR-15cxla-miR-428
NC_030737.1:18147566–18150411-xla-miR-363xla-miR-133dxla-miR-133axla-miR-133bxla-miR-142
NC_030728.1:15545322–15553229+xla-miR-1bxla-miR-205
NC_030734.1:87183400–87183864+xla-miR-1306
NC_030724.1:170644099–170647782+xla-miR-427xla-miR-428xla-miR-205xla-miR-19b
NC_030732.1:52962177–52964782-xla-miR-18
NC_030738.1:104708016–104708272-xla-miR-23a
NC_030739.1:67484971–67488099-xla-miR-427xla-miR-15cxla-miR-428xla-miR-429xla-miR-194
NC_030726.1:10872555–10886282-xla-miR-223
NC_030724.1:117241997–117249358-xla-miR-18
NC_030727.1:78958172–78962369+xla-miR-15cxla-miR-142xla-miR-1bxla-miR-19bxla-miR-427
NC_030727.1:18870001–18886389-xla-miR-133axla-miR-133dxla-miR-133bxla-miR-15cxla-miR-427
NC_030733.1:135732775–135754096+xla-miR-15cxla-miR-133axla-miR-133bxla-miR-133dxla-miR-429
NC_030727.1:19553660–19564667-xla-miR-18xla-miR-20
NW_016694812.1:6029247-6039595+xla-miR-703
NC_030726.1:153409169–153409658-xla-miR-92a
NC_030727.1:3769521–3772178-xla-miR-142xla-miR-19bxla-miR-15c
NC_030734.1:67440735–67446103-xla-miR-427xla-miR-428xla-miR-23axla-miR-18xla-miR-24b
NC_030734.1:149012368–149016101+xla-miR-1b
NC_030725.1:12051270–12078805+xla-miR-15c
NC_030726.1:166923803–166925161+xla-miR-1bxla-miR-363xla-miR-1306
NC_030741.1:271408–272630-xla-miR-205
NC_030730.1:17790904–17795162+xla-miR-1bxla-miR-205
NC_030732.1:150988305–150989939+xla-miR-1b
NC_030727.1:18890380–18893603-xla-miR-427xla-miR-19bxla-miR-428xla-miR-15cxla-miR-20
NC_030740.1:27551656–27584622+xla-miR-20xla-miR-142xla-miR-428xla-miR-1bxla-miR-427
NC_030741.1:9140397–9144563+xla-miR-18xla-miR-428xla-miR-20xla-miR-19bxla-miR-1b
NC_030740.1:85534431–85552303+xla-miR-18xla-miR-205xla-miR-19bxla-miR-194
circRNAmiRNAmiRNAmiRNAmiRNAmiRNA
NC_030724.1:17377459–17378170-xla-miR-92a
NC_030740.1:36131571–36138031+xla-miR-428xla-miR-18xla-miR-223xla-miR-20
NC_030741.1:101502504–101504659+xla-miR-15c
NC_030740.1:64855970–64900296+xla-miR-194xla-miR-205xla-miR-19bxla-miR-24bxla-miR-18
NC_030733.1:2015378–2022047-xla-miR-223xla-miR-205
NC_030734.1:110966435–110974339-xla-miR-1b
NC_030734.1:91534606–91543234-xla-miR-15cxla-miR-20xla-miR-363xla-miR-194xla-miR-18
NC_030737.1:30055193–30055397-xla-miR-429
NC_030731.1:77496813–77500806-xla-miR-427
NC_030735.1:34874500–34913276-xla-miR-15cxla-miR-427xla-miR-20xla-miR-18xla-miR-133a
NC_030728.1:55711908–55719138-xla-miR-15cxla-miR-1b
NC_030730.1:87340543–87345501-xla-miR-427xla-miR-428
NC_030728.1:103167247–103175214+xla-miR-23a
NC_030730.1:38529852–38532217-xla-miR-23axla-miR-205xla-miR-1b
NC_030736.1:79090419–79096019+xla-miR-427xla-miR-428xla-miR-20
NC_030736.1:90287438–90296330-xla-miR-19bxla-miR-15cxla-miR-92axla-miR-133axla-miR-20
NC_030730.1:8539270–8539599-xla-miR-205
NC_030725.1:82906739–82912357+xla-miR-223xla-miR-703xla-miR-20xla-miR-194xla-miR-92a
NC_030740.1:111007219–111015557-xla-miR-205xla-miR-427
NC_030724.1:143889932–143891419+xla-miR-15cxla-miR-427
NC_030740.1:70765471–70766361-xla-miR-1bxla-miR-205xla-miR-1306
NC_030727.1:28031557–28054001-xla-miR-205
NC_030738.1:21875834–21876319+xla-miR-15c
NC_030731.1:70524254–70525545-xla-miR-205
NC_030729.1:48857151–48875366-xla-miR-142
NC_030729.1:95566328–95569412-xla-miR-23axla-miR-1bxla-miR-20xla-miR-92axla-miR-427
NC_030727.1:60094099–60097903-xla-miR-429xla-miR-223xla-miR-194
NC_030736.1:77709534–77736150+xla-miR-23axla-miR-18xla-miR-205xla-miR-15c
NC_030740.1:85858236–85862849+xla-miR-15cxla-miR-427xla-miR-142xla-miR-1bxla-miR-133a
NW_016694815.1:4530866-4536613+xla-miR-133axla-miR-133bxla-miR-133d
NC_030725.1:127078532–127083938+xla-miR-15c
NC_030724.1:210401341–210403176-xla-miR-15cxla-miR-427xla-miR-142xla-miR-428
NC_030725.1:163811669–163814745+xla-miR-15c
NC_030734.1:46013983–46031765-xla-miR-23axla-miR-1b
NC_030726.1:156345869–156347774-xla-miR-18
NC_030734.1:113723725–113729935+xla-miR-92axla-miR-19bxla-miR-15cxla-miR-205xla-miR-1b
Sequences of primers in the Q-RT-PCR assay for validating the differential expressions of circRNAs after sequencing. The results of Q-RT-PCR validation of the differentially expressed circRNAs. Sequences of the primers used were listed in Table 1. The enrichment pathways of differentially expressed circRNAs-associated target genes by KEGG. The top 5 predicted miRNA targets for 282 circRNAs linked to X. laevis exposed to 100 µg/L AZ for 180 days.

Experimental design, materials and methods

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 calculated according to the 2-△△CT method [6]. The upregulated circRNAs were identified at 2-△△CT >1, the downregulated circRNAs were identified at 2-△△CT<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< 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).
Subject areaEnvironmental toxicology
More specific subject areaCircRNA study involved in developing male Xenopus laevis chronically exposed to 100 µg/L AZ
Type of dataTable
How data was acquiredQuantitative RT-PCR (ViiA 7 Real-time PCR System, Applied Biosystems, Carlsbad, CA, USA), Kyoto Encyclopedia of Genes and Genomes (KEGG), miRNA-binding sites on circRNAs are predicted by custom-written software based on Targetscan and Miranda software (Cloud-Seq Biotech Ltd. Co., Shanghai, China)
Data formatAnalyzed
Experimental factorscDNA amplification, RNA library construction, RNA-sequencing, PCR analysis, bioinformatics analysis
Experimental featuresValidation of differentially expressed circRNAs by Q-RT-PCR, KEGG analysis of differentially expressed circRNA-associated target genes and prediction of miRNA binding sites
Data source locationJi’nan, Shandong, China
Data accessibilityThis is an innovative data, not yet published elsewhere
Related research articleIdentification of circular RNAs and their alterations involved in developing male X. laevis chronically exposed to AZ.
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