Individual genotyping of caged red foxes from the analysis of 14 microsatellite targets and one sex marker

Description of the dataset
Individual genotyping of caged red foxes (H for hair, F for faeces) from the analysis of 14 microsatellite targets (AHT121, AHT137, C01.424, INU055, AHTh171, C08.618, CPH2, FH2010, C04.140, CXX0279, FH2848, REN169O18, CPH11, FH2457) and one sex marker (K9-AMELO) (Breen et al., 2001; Fredholm and Winterø, 1995; Holmes et al., 1995; Ichikawa et al., 2002; Moore et al., 2010; Ostrander et al., 1993)
ND for no data.
The experimental station of the French National Reference Laboratory (NRL) at the ANSES laboratory (Atton, Meurthe-et-Moselle, France) provided 20 hair samples and 20 faecal samples taken in pairs from caged red foxes (n = 20; 10 females, 10 males). The faecal samples were collected shortly after deposition in the animal cages. To avoid cross-contamination, all samples were placed separately in individual sealed bags and frozen at – 20°C until laboratory analyses.
Genomic DNA was extracted from hair root using the Qiagen DNeasy tissue kit (Qiagen, Hilden, Germany) following the manufacturer’s recommendations. The QIAmp Fast DNA Stool kit (Qiagen, Hilden, Germany) was used to extract genomic DNA from faecal samples.
Fragment size analyses were performed to obtained allele size quantification for the 14 microsatellites and the sex marker, by using a SeqStudio Genetic Analyzer (Applied Biosystems, Foster City, CA). Genetic profiles were determined using the Microsatellite Analysis module available on the Thermo Fisher cloud (https://apps.thermofisher.com/editor-web/#/app/app-microsatellites-web).

References
Breen, M., Jouquand, S., Renier, C., Mellersh, C.S., Hitte, C., Holmes, N.G., Chéron, A., Suter, N., Vignaux, F., Bristow, A.E., Priat, C., McCann, E., André, C., Boundy, S., Gitsham, P., Thomas, R., Bridge, W.L., Spriggs, H.F., Ryder, E.J., Curson, A., Sampson, J., Ostrander, E.A., Binns, M.M., Galibert, F., 2001. Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Res. 11, 1784–1795.
Fredholm, M., Winterø, A.K., 1995. Variation of short tandem repeats within and between species belonging to the Canidae family. Mamm. Genome Off. J. Int. Mamm. Genome Soc. 6, 11–18.
Holmes, N.G., Dickens, H.F., Parker, H.L., Binns, M.M., Mellersh, C.S., Sampson, J., 1995. Eighteen canine microsatellites. Anim. Genet. 26, 132–133.
Ichikawa, Y., Takahashi, Y., Tsumagari, S., Takeishi, M., Ishihama, K., Morita, M., Kanemaki, M., Minezawa, M., Takahashi, H., 2002. Identification and characterization of 40 dinucleotide microsatellites in the dog genome. Anim. Genet. 33, 400–401.
Moore, M., Brown, K.S., Sacks, A., 2010. Thirty-one short red fox (Vulpes vulpes) microsatellite markers. Mol. Ecol. Resour. 10, 404–408.
Ostrander, E.A., Sprague, G.F., Rine, J., 1993. Identification and characterization of dinucleotide repeat (CA)n markers for genetic mapping in dog. Genomics 16, 207–213.

数据集说明
本数据集针对圈养赤狐开展个体基因分型（毛发样本标记为H，粪便样本标记为F），通过对14个微卫星（microsatellite）靶点（AHT121、AHT137、C01.424、INU055、AHTh171、C08.618、CPH2、FH2010、C04.140、CXX0279、FH2848、REN169O18、CPH11、FH2457）及1个性别标记（K9-AMELO）进行分析构建（参考文献：Breen等，2001；Fredholm与Winterø，1995；Holmes等，1995；Ichikawa等，2002；Moore等，2010；Ostrander等，1993）。
ND表示无有效数据。
ANSES实验室下属的法国国家参考实验室（NRL）实验站（位于法国默尔特-摩泽尔省阿通市），提供了20对取自20只圈养赤狐的毛发样本与粪便样本（总样本量n=20，其中雌性、雄性个体各10只）。粪便样本于排泄后即刻在笼舍内采集。为避免交叉污染，所有样本均单独封装于密封袋中，并保存于-20℃环境直至实验室分析。
研究人员按照厂商说明书，使用凯杰（Qiagen，德国希尔登）DNeasy组织试剂盒从毛发根部提取基因组DNA（Genomic DNA）；粪便样本的基因组DNA提取则采用凯杰（Qiagen，德国希尔登）QIAamp Fast DNA Stool试剂盒。
通过SeqStudio基因分析仪（应用生物系统公司，美国加利福尼亚州福斯特城）对14个微卫星及性别标记开展片段长度分析，以实现等位基因长度定量。各样本的基因型谱通过赛默飞世尔云平台上的微卫星分析模块（Microsatellite Analysis module）确定，平台网址为https://apps.thermofisher.com/editor-web/#/app/app-microsatellites-web。

参考文献
1. Breen, M.等，2001. 染色体特异性单座位荧光原位杂交（FISH）探针可将包含1800个标记的家犬基因组整合辐射杂交/连锁图谱锚定至所有染色体。《基因组研究（Genome Res.）》，11卷，1784–1795页。
2. Fredholm, M.，Winterø, A.K.，1995. 犬科物种内及物种间的短串联重复序列变异。《国际哺乳动物基因组学会官方期刊·哺乳动物基因组（Mamm. Genome Off. J. Int. Mamm. Genome Soc.）》，6卷，11–18页。
3. Holmes, N.G.等，1995. 十八个犬类微卫星标记。《动物遗传学（Anim. Genet.）》，26卷，132–133页。
4. Ichikawa, Y.等，2002. 犬基因组中40个二核苷酸微卫星的鉴定与表征。《动物遗传学（Anim. Genet.）》，33卷，400–401页。
5. Moore, M.等，2010. 三十一个赤狐（Vulpes vulpes）微卫星标记。《分子生态资源（Mol. Ecol. Resour.）》，10卷，404–408页。
6. Ostrander, E.A.等，1993. 犬遗传作图用二核苷酸重复(CA)n标记的鉴定与表征。《基因组学（Genomics）》，16卷，207–213页。