Umbilical cord blood methylome analysis of IVF neonates that underwent embryo culture in G5 or HTF medium. Umbilical cord blood methylome analysis of IVF neonates that underwent embryo culture in G5 or HTF medium

Follow-up study of IVF neonates who underwent embryo culture in G5 (Vitrolife) or HTF (Lonza) medium. Genome-wide DNA methylation profiling of IVF neonates (umbilical cord blood samples) who had undergone embryo culture in G5 medium (Vitrolife) or HTF medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome. Overall design: Bisulphite converted DNA from umbilical cord blood samples from IVF neonates that had undergone embryo culture in G5 (n = 59 ) or HTF (n = 47) culture medium, were hybridized to the Illumina EPIC array. Data processing was conducted in R using the RnBeads package. Processing consisted of SWAN normalization, and site/sample removal based on greedycut (detection p-value threshold 0.05), SNP proximity, position on the sex chromosomes, missing values in >5% of samples and sites not in a CpG context.

本数据集针对使用G5（Vitrolife公司）或HTF（Lonza公司）培养基进行胚胎培养的体外受精（In Vitro Fertilization, IVF）新生儿开展研究，包含两项核心内容：其一为该类IVF新生儿的随访研究，其二为针对使用上述两种培养基培养的IVF新生儿（采集脐血样本）开展的全基因组DNA甲基化谱分析。研究采用EPIC芯片对人类基因组上约85万个CpG位点的甲基化组进行谱解析。

实验设计方案如下：将使用G5培养基（n=59）或HTF培养基（n=47）进行胚胎培养的IVF新生儿的脐血亚硫酸氢盐转化DNA，与Illumina EPIC芯片进行杂交。数据分析采用R语言中的RnBeads软件包完成，具体流程包含SWAN归一化，以及基于以下标准剔除位点和样本：greedycut算法（检测P值阈值为0.05）、单核苷酸多态性（Single Nucleotide Polymorphism, SNP）邻近区域、性染色体上的位点、在超过5%的样本中存在缺失值的位点，以及非CpG背景的位点。