High-resolution Hi-C profiling of human breast tissues using an optimized protocol for clinical samples

Here, we present an optimized high-resolution Hi-C protocol for human breast tissues using the Phase Genomics Proximo Hi-C Kit. We describe steps for liquid nitrogen tissue processing, crosslinking, and quenching, followed by cell lysis and controlled chromatin fragmentation. Proximity ligation captures three-dimensional interactions, followed by reverse crosslinking, DNA purification, and streptavidin bead enrichment. Libraries are prepared on beads, amplified, and cleaned with size selection, producing high-quality material for Illumina sequencing and genome-wide 3D chromatin analysis. For complete details on the use and execution of this protocol, please refer to Choppavarapu et al. 1 • An optimized protocol for Hi-C library preparation from human breast tissues • Preserves native chromatin interactions via controlled tissue processing • Enzymatic fragmentation and proximity ligation to capture spatial chromatin organization • Quality control to ensure high-quality Hi-C libraries suitable for sequencing Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we present an optimized high-resolution Hi-C protocol for human breast tissues using the Phase Genomics Proximo Hi-C Kit. We describe steps for liquid nitrogen tissue processing, crosslinking, and quenching, followed by cell lysis and controlled chromatin fragmentation. Proximity ligation captures three-dimensional interactions, followed by reverse crosslinking, DNA purification, and streptavidin bead enrichment. Libraries are prepared on beads, amplified, and cleaned with size selection, producing high-quality material for Illumina sequencing and genome-wide 3D chromatin analysis.