Data from: DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

The number of children born since the origin of Assisted Reproductive
Technologies (ART) exceeds 5 million. The majority seem healthy, but a
higher frequency of defects has been reported among ART-conceived infants,
suggesting an epigenetic cost. We report the first whole-genome DNA
methylation datasets from single pig blastocysts showing differences
between in vivo and in vitro produced embryos. Blastocysts were produced
in vitro either without (C-IVF) or in the presence of natural reproductive
fluids (Natur-IVF). Natur-IVF embryos were of higher quality than C-IVF in
terms of cell number and hatching ability to. RNA-Seq and DNA methylation
analyses showed that Natur-IVF embryos have expression and methylation
patterns closer to in vivo blastocysts. Genes involved in reprogramming,
imprinting and development were affected by culture, with fewer
aberrations in Natur-IVF embryos. Methylation analysis detected methylated
changes in C-IVF, but not in Natur-IVF, at genes whose methylation could
be critical, such as IGF2R and NNAT.