High-Depth Meta-Hi-C Chromatin Contact Matrices for Three Species

Aggregated chromatin contact matrices were built from 3,619 Human, 6,732 Mouse, and 487 Fly Hi-C experimental runs. The dataset provides intrachromosomal (cis) and interchromosomal (trans) contact matrices at 10KB and 1KB resolutions, stored in HiCMatrix format. Author Ruchi Lohia published this resource in March 2026.

Use Cases

• Predict gene coexpression relationships by analyzing contact frequencies in the cis chromatin interaction matrices at 10KB resolution.
• Identify potential enhancer-promoter links by modeling long-range functional relationships captured in the trans contact matrices.
• Train models to infer cross-species chromatin architecture conservation using the aggregated Human, Mouse, and Fly meta-Hi-C matrices.
• Validate or benchmark eQTL (expression quantitative trait loci) predictions using the high-depth genome-wide contact data.

Strengths

• Aggregates 10,838 total Hi-C experimental runs (3,619 Human + 6,732 Mouse + 487 Fly) for high statistical power.
• Provides contact matrices at two resolutions (10KB and 1KB) for detailed analysis of chromatin interactions.
• Large-scale dataset totaling 83.1 GB, enabling analysis of long-range genomic relationships.

Limitations

• Sample size for Fly (487 runs) is significantly smaller than for Human and Mouse, limiting comparative power for that species.
• Data is stored in a specialized HiCMatrix (.h5) format, requiring specific tools like HiCExplorer for access and analysis.
• No direct row or column counts are provided for the matrices, making initial data sizing ambiguous.

Provenance

Source

Hi-C runs were obtained from the Sequence Read Archive (SRA) with species and experiment strategy filters.

Collection Method

Reads from each Hi-C run were aligned to reference genomes (hg38, mm10, dm6) and aggregated to create species-specific meta-Hi-C matrices.

Freshness

Last updated March 2026.