Comprehensive 100-bp resolution genome-wide epigenomic profiling data for the hg38 human reference genome

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• The human genome's epigenomic landscape is crucial for understanding gene regulation and biological processes.
• Existing epigenomic datasets often lack comprehensive coverage or standardized processing.
• The Encyclopedia of DNA Elements (ENCODE) consortium has generated vast amounts of sequencing data.

Purpose of the Study:

• To create a unified, high-resolution (100-bp) genome-wide epigenomic dataset for the human genome.
• To provide a standardized and accessible resource for researchers studying epigenetics and gene regulation.
• To develop a replicable data processing pipeline for epigenomic assays.

Main Methods:

• Processed raw sequencing data from five ENCODE assay types: DNase-seq, ChIP-seq (histone and TF), ATAC-seq, and Poly(A) RNA-seq.
• Filtered data for quality, merging technical replicates by averaging read counts into 100-bp bins across the genome.
• Developed a tabix-indexed dataset for efficient retrieval of read counts by genomic coordinates.

Main Results:

• Generated 6,305 high-quality, genome-wide epigenomic profiles at 100-bp resolution.
• Created a comprehensive dataset covering approximately 30 million 100-bp genomic bins.
• Provided an example of integrating epigenomic data with disease-risk variants from the GWAS Catalog.

Conclusions:

• The processed epigenomic data serve as valuable features for statistical and machine learning models.
• These data facilitate novel insights into gene expression, chromatin accessibility, and epigenetic modifications.
• The presented data processing pipeline is adaptable for other genome-wide assays, enhancing data accessibility and utility.