Center for Epigenomics:
Single-cell Epigenomics Platform

The Single-cell Epigenomics Platform uses state-of-the-art single cell multiomic sequencing methods to resolve the cellular heterogeneity of the epigenome, transcriptome, and 3D genome architecture. Such technologies include single cell RNA-seq and ATAC-seq and single nucleus methyl-3C. A major focus is to make these assays as widely applicable as possible by optimizing sample preparation for fresh and frozen tissues, cell lines and clinical biopsies. To this end, the single cell epigenomics platform and its staff have established workflows to generate high-quality data for dozens of human tissues including brain, heart, kidney, lung, pancreas, adipose, tumors, organoids, and cell types as well as workflows for evaluation of experimental conditions to generate high-quality data for novel sample types.

We are continually optimizing our assays to increase robustness and throughput to achieve higher quality at lower costs. We’ve successfully utilized these technologies to gain novel insights on how the epigenome and 3D genome promotes development, neurological diseases, and mammalian evolution.

Below are descriptions of our most commonly used or latest methods.

Single-cell ATAC-seq:
To resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types, we analyze the transposase-accessible chromatin in single-nuclei that have been isolated from tissue samples. We employ both an in-house, semi-automated robust platform using combinatorial barcoding (single cell indexing, sciATAC-seq) and the commercial droplet based single cell ATAC-seq approach from 10x Genomics with standard operating procedures. Depending on the sample type, research and budget we will work with collaborators to identify customized solutions and recommendations for each project.

Single-cell RNA-seq:
To identify and characterize distinct cell types from heterogeneous biological samples (including frozen tissue biopsies), we use single cell and single nucleus RNA-seq. By combining flow cytometry with the 10x Genomics Chromium Platform, we can profile the RNA expression profile of thousands of cells or nuclei.

Single-nucleus Methyl-3C sequencing (snm3C-seq): 
To delineate the heterogeneous relationship between chromatin architecture and DNA methylation status in mixed cellular populations. This is achieved by profiling both DNA methylation and 3D chromatin contacts from the same cell, giving cell type/state resolved epigenome and genome organization information from complex tissues. DNA methylation profiles are highly cell type and context specific and effective in resolving cell types by Single-Cell clustering methods. DNA methylation is a dynamic epigenetic modification that plays roles in development and disease. Regulatory regions, such as promoters and enhancers, are generally hypomethylated when active and mark the binding of regulatory proteins that influence gene expression. In the same cell, this assay additionally provides chromatin contact information to reconstruct the 3D genome organization. The organization of the genome informs gene regulatory programs such as close proximity of distal regulatory elements to their target genes, even when far away in the linear genome. Coupling both modalities in the same cell allows for higher resolution Single-Cell clustering and more accurate cell type identification.