droplet based high efficient chromatin conformation capture (DropHiChew)
Our research is focused on finding practical and cost-effective ways to extend our knowledge of the DNA dynamic movement. We've put to use the 10X single-cell systems to develop a user-friendly, droplet-based chromatin conformation capture technique called DropHiChew. This efficient process involves digesting single nuclei with enzymes, ligating nearby fragments, attaching adaptor sequences using Tn5, and packaging single cells with barcode gel beads via the 10X chromium system. After this, we carry out in-droplet reverse crosslinking and label each nucleus DNA with a barcode through linear amplification. Given that the 10X single cell system usually yields thousands of cells, a budget of 2M per cell could be beyond the budget for many labs. To capture the movement of DNA in depth, we've crafted a new algorithm, loop velocity, based on loop extrusion models. Our research indicates that even with shallow sequencing (50k contacts per cells), we can accurately gauge the speed and direction of cell development using our loop velocity algorithm. We're confident that this method has great potential for diverse applications in future chromatin capture studies.