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Single Cell Epigenomics Services

Our automated technology platforms enable cost-effective workflows to incorporate epigenomics into a variety of research projects. In some cases, we can offer epigenomic assays on a fee-for-service basis. Please see below for the single cell services available at the Center on a fee-for-service basis.


Single Cell Services

The Center for Epigenomics has 3 single cell genomics assays available for Epigenomic Services: sci-ATAC-seq, 10x-ATAC-seq, and 10x-sc/snRNA-seq.  Review each assay's unique characteristics in the details below to determine which assay best fits your research needs.

sci-ATAC-seq

sci-ATAC-seq (single cell combinatorial indexing) originally developed by Jay Shendure's lab (Cusanovich et al. 2015) to resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. This platform offers high flexibility e.g. the ability to mix multiple samples in one run as well as the opportunity to run a small-scale experiment to identify best conditions or to evaluate sample quality. We usually capture ~10k nuclei per 96 well plate (these can be split between samples and/or conditions). After completion of the assay we will provide a data report based on our processing pipeline.

Example publications:

Human lung tissue

Mouse brain

Mouse mammary gland cells

Whole mouse embryo

Pancreatic islets

10x-ATAC-seq

A droplet based single cell ATAC-seq platform from 10x Genomics (Satpathy et al. 2019) used to resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types.  This platform works particularly well for cell lines, tissue with minimal debris, and samples with a low number of starting cells/nuclei.  After the completion of the assay we will provide a standard Cell Ranger data report for each sample.

Example publications:

Please check back later for example publication

10x-sc/snRNA-seq 

We use the droplet-based 10x Genomics Chromium Platform to generate 3'RNA expression profiles of thousands of cells or nuclei (Zheng et al. 2017). For other RNA expression profiling solutions, e.g. 5' profiling please contact us at epigenome@ucsd.edu.  After completion of the assay we will provide a standard Cell Ranger data report for each sample.

Example publications:

Brain organoids

Human Lung


How do I initiate a single cell services project with the Center for Epigenomics?

All samples submitted for our single cell assays follow a typical workflow:

If you are interested in our single cell Services, please contact us at epigenome@ucsd.edu to discuss your ideas.


Looking for specific information about single cell assays with the Center?


FAQs

Project Generation

Sample Preparation

Sample Submission

Sample Processing

Project Completion

Other Questions


Contact info

epigenome@ucsd.edu

CMM-East
Room #1056-8 (Offices)
Room #1087-88 (Labs)