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| Status |
Public on Sep 24, 2017 |
| Title |
In vitro procedures exacerbate chromosome instability in early cleavage stage embryos |
| Organism |
Bos taurus |
| Experiment type |
SNP genotyping by SNP array
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| Summary |
Chromosomal instability (CIN) occurs at high frequency during early in vitro embryogenesis and is known to be associated with early embryonic loss in humans. The chromosomal stability of in vivo-conceived cleavage stage embryos largely remains unknown. Here, we applied haplotyping and copy number profiling to investigate genomic architecture of 171 single bovine blastomeres and to compare the nature and frequency of CIN between in vivo embryos, in vitro embryos produced from ovum pick up with ovarian stimulation (OPU-IVF), and in vitro produced embryos from in vitro matured oocytes without ovarian stimulation (IVM-IVF). Our data shows that CIN is significantly lower in in vivo conceived cleavage stage embryos when compared to in vitro cultured embryos, as genomic stability of single blastomeres in both IVF embryos was severely compromised (P<0.0001)
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| Overall design |
Five young healthy, cycling Holstein Friesian heifers (Bos Taurus) were used as donors for oocytes and embryos. The semen from the same bull was used for embryo production in all five cows. Blood samples from the donor cows (mothers) and semen from the bull (father) were used to extract bulk DNA (DNeasy Blood and Tissue kit, Qiagen, Germany). Bulk DNA was also obtained from the parents of the bull (paternal grandparents) and from the available parents of cows (maternal grandparents; only for crosses 4757, 8301 and 9617). All cows were submitted to hormonal stimulation with subsequent ovum pick up or in vivo embryo collection. After hormonal treatments, cows were left untreated for a month before they were slaughtered. Ovaries were collected separately and retrieval of the oocytes was followed by routine in vitro embryo production. The embryos were treated with pronase to dissolve zona pellucida and single blastomeres were retrieved from zona free embryos and whole-genome amplified (WGA) using commercial multiple displacement amplification kit (Repli-G Single Cell kit, Qiagen). WGA products and bulk parental and grandparental DNA were then SNP genotyped on BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA). Subsequently, the SNP logR and SNP B-allele frequency (BAF) values, as well as the discrete SNP genotype calls were obtained for each single cell and applied in further single-cell analysis to obtain genome-wide haplarithm profiles using a modified version of the siCHILD algorithm (Zamani Esteki et al. 2015).
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| Contributor(s) |
Tšuiko O, Catteeuw M, Zamani Esteki M, Destouni A, Bogado Pascottini O, Besenfelder U, Havlicek V, Smits K, Kurg A, Salumets A, D’Hooghe T, Voet T, Van Soom A, Vermeesch JR |
| Citation(s) |
29040498 |
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| Submission date |
Feb 24, 2017 |
| Last update date |
Oct 19, 2017 |
| Contact name |
Masoud Zamani Esteki |
| E-mail(s) |
masoud.zamaniesteki@mumc.nl
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| Phone |
+31 43 38 75306
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| Organization name |
Maastricht University Medical Center
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| Department |
Clinical Genetics
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| Lab |
Cellular Genomic Medicine
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| Street address |
P. Debyelaan 25
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| City |
Maastricht |
| State/province |
Limburg |
| ZIP/Postal code |
6229 HX |
| Country |
Netherlands |
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| Platforms (1) |
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| Samples (236)
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| Relations |
| BioProject |
PRJNA377907 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95358_RAW.tar |
2.5 Gb |
(http)(custom) |
TAR (of IDAT) |
| Processed data included within Sample table |
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