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Single-Cell Epigenetic State Profiling and Analysis with ATAC-seq In Complex Human Tissue

Focus Gastrointestinal

Project Goal

To generate validated workflows for generation and analysis of high-quality single-cell and bulk chromatin accessibility data sets.

Results & Resources

During this project, the Greenleaf lab made improvements to the scATAC-seq protocol: the protocol was optimized and is now usable with the 10X chromium platform, as well as details on nuclei isolation for the method; usage was extended beyond blood to the liver, brain and skin; and computational metrics for quality control and data processing were produced. Their method for protein-indexed ATAC-seq (Pi-ATAC) that combines single-cell chromatin and proteomic profiling is available on


Lead Investigator

William Greenleaf
William Greenleaf