DOI: 10.5061/dryad.n77r3
title: Data from: DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

description: 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.
description: lane3276_CGATGTTT_54re_L006_trimmed_tophatRNA-seq data embryo #54lane3276_TGACCACT_93re_L006_trimmed_tophatRNA-Seq data embryo #93lane3276_TTAGGCAT_60re_L006_trimmed_tophatRNA-Seq data embryo #60lane3277_ACAGTGGT_94re_L007_trimmed_tophatRNA-Seq data embryo #94lane3277_ACTTGATG_191re_L007_trimmed_tophatRNA-Seq data embryo #191lane3277_ATCACGTT_190re_L007_trimmed_tophatRNA-Seq data embryo #190lane3277_CAGATCTG_189re_L007_trimmed_tophatRNA-Seq data embry #189lane3277_GCCAATGT_96re_L007_trimmed_tophatRNA-Seq data embryo #96lane3276_ATCACGTT_27re_L006_trimmed_tophatRNA-Seq data embro #27CpG_CTOB_lane1_34_TGACCACT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #34CpG_CTOT_lane1_34_TGACCACT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #34_2CpG_CTOB_lane1_35_CGATGTTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #35CpG_CTOT_lane1_35_CGATGTTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #35_2CpG_CTOB_lane1_36_ATCACGTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #36CpG_CTOT_lane1_36_ATCACGTT_L001_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #36_2CpG_CTOB_lane2_55_ACTTGATG_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #55CpG_CTOT_lane2_55_ACTTGATG_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #55_2CpG_CTOB_lane2_85_CGATGTTT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #85CpG_CTOT_lane2_85_CGATGTTT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #85_2CpG_CTOB_lane2_86_TGACCACT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #86CpG_CTOT_lane2_86_TGACCACT_L002_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #86_2CpG_CTOB_lane6_186_TGACCACT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methyation data embryo #186CpG_CTOT_lane6_186_TGACCACT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #186_2CpG_CTOB_lane6_193_ACAGTGGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #193CpG_CTOT_lane6_193_ACAGTGGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #193_2CpG_CTOB_lane6_197_GCCAATGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #197CpG_CTOT_lane6_197_GCCAATGT_L006_R1_trimmed.fq.gz_bismark_bt2.deduplicated.txtDNA methylation data embryo #197_2