Welcome to Pig Matrix, the first systematically constructed 3D regulatory genomics database for the pig (Sus scrofa). Built on a standardized experimental framework, Pig Matrix database integrates matched multi-omics datasets across diverse tissues, developmental stages, and porcine cell lines. By integrating epigenomic and 3D genome information, the database connects proximal and distal cis-regulatory elements to their target genes, thereby facilitating functional interpretation of non-coding variants and genomic signals in evolutionary and comparative studies. In addition to data retrieval, visualization, genome browsing, and download, Pig Matrix provides dedicated resource modules for evolutionary and comparative analyses, and is further extended with xenotransplantation-related resources and potential utility for future AI-oriented applications in regulatory genomics.
Well-defined donor：All data originate from 8 genetically and phenotypically characterized pigs.
Parallel multi-omics generation：Each of the 94 biological samples was systematically profiled across all omics layers, resulting in 1,170 experimental datasets.
Unified Protocol & Pipeline
Comprehensive Spatiotemporal Coverage
Temporal Dimension: Covers 4 major developmental stages.
Spatial Dimension: Encompasses 11 major organs and 3 widely utilized cell lines.
Multi-Omics and 3D Genome Structure
Genome: Detection of SNPs, InDels, and structural variants.
Epigenome: Profiling of DNA methylation, chromatin accessibility, 7 histone modifications and 2 transcription factor binding.
3D genome: Systematic identification of higher-order chromatin structures including A/B compartments, TADs, and loops
Transcriptome
Single-cell omics: snRNA-seq profiling of 3 major donor organs.
Functional Annotation of the Genome
Cis-regulatory elements (CREs): Identification of 1,067,540 CREs, bringing to the level of model organisms.
Element–gene interactions: Mapping proximal/distal element and gene regulatory connections.