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.
lane3276_CGATGTTT_54re_L006_trimmed_tophat
RNA-seq data embryo #54
lane3276_TGACCACT_93re_L006_trimmed_tophat
RNA-Seq data embryo #93
lane3276_TTAGGCAT_60re_L006_trimmed_tophat
RNA-Seq data embryo #60
lane3277_ACAGTGGT_94re_L007_trimmed_tophat
RNA-Seq data embryo #94
lane3277_ACTTGATG_191re_L007_trimmed_tophat
RNA-Seq data embryo #191
lane3277_ATCACGTT_190re_L007_trimmed_tophat
RNA-Seq data embryo #190
lane3277_CAGATCTG_189re_L007_trimmed_tophat
RNA-Seq data embry #189
lane3277_GCCAATGT_96re_L007_trimmed_tophat
RNA-Seq data embryo #96
lane3276_ATCACGTT_27re_L006_trimmed_tophat
RNA-Seq data embro #27
CpG_CTOB_lane1_34_TGACCACT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #34
CpG_CTOT_lane1_34_TGACCACT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #34_2
CpG_CTOB_lane1_35_CGATGTTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #35
CpG_CTOT_lane1_35_CGATGTTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #35_2
CpG_CTOB_lane1_36_ATCACGTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #36
CpG_CTOT_lane1_36_ATCACGTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #36_2
CpG_CTOB_lane2_55_ACTTGATG_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #55
CpG_CTOT_lane2_55_ACTTGATG_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #55_2
CpG_CTOB_lane2_85_CGATGTTT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #85
CpG_CTOT_lane2_85_CGATGTTT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #85_2
CpG_CTOB_lane2_86_TGACCACT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #86
CpG_CTOT_lane2_86_TGACCACT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #86_2
CpG_CTOB_lane6_186_TGACCACT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methyation data embryo #186
CpG_CTOT_lane6_186_TGACCACT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #186_2
CpG_CTOB_lane6_193_ACAGTGGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #193
CpG_CTOT_lane6_193_ACAGTGGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #193_2
CpG_CTOB_lane6_197_GCCAATGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #197
CpG_CTOT_lane6_197_GCCAATGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txt
DNA methylation data embryo #197_2