3CDB

3CDB provides a curated database of chromosome conformation capture (3C) experimental data to support analysis of chromatin interactions and three-dimensional genome organization.

Key Features:

• Curated 3C Data Repository: Contains experimentally validated chromosome conformation capture (3C) datasets describing chromatin interactions within genomic regions.
• Quantitative Interaction Measurement Data: Includes interaction frequency measurements obtained using real-time PCR with TaqMan probes for estimating ligation frequencies.
• Integration of Related Chromatin Interaction Methods: Incorporates datasets from related techniques including ChIP-loop assays and chromosome conformation capture derivatives such as 4C and 5C.
• Chromatin Interaction Information: Provides qualitative and quantitative data describing spatial chromatin interactions across genomic loci.

Scientific Applications:

• 3D Genome Organization Studies: Supports investigation of spatial chromatin architecture and long-range genomic interactions.
• Gene Regulation Research: Enables analysis of chromatin interactions associated with gene regulatory elements.
• Epigenomics and Chromatin Biology: Facilitates studies integrating chromatin conformation with chromatin immunoprecipitation-derived interaction data.

Methodology:

The underlying chromosome conformation capture method cross-links interacting genomic loci with formaldehyde, digests chromatin with restriction enzymes, ligates interacting fragments, and quantifies ligation products using real-time PCR with TaqMan probes to measure chromatin interaction frequencies.