ZHANG LAB

The high-throughput sequencing datasets characterized typical omics (i.e., transcriptomics, epigenomics of DNA methylation, chromatin accessibility and three types of histone modifications) in mouse and human germline cycle are collected from a public database (Gene Expression Omnibus, GEO). To represent and investigate the transcriptional regulatory effects of epigenetic modifications, we focused on the gene promoter regions, defined as those regions -2,000 base pairs (bp) and +500 bp around the transcription start sites. For these datasets with preprocessed data available, the preprocessed expression levels or the signals of epigenetic features were adopted. For those datasets that had only raw data available, raw reads were first trimmed using TrimGalore and then mapped to the reference genome (mm9 for mouse and hg19 for human). For RNA-seq data, the sequenced reads were mapped to the reference genome using TopHat (v2.1.1) with default parameters. To make the expressions comparable..