Chromatin Profiling Analysis


Chromatin compaction/accessibility, as well as histone post-translational modifications (PTMs) and the full repertoire of chromatin-associated proteins, define the chromatin state in any region of the genome. This Chromatin state is the primary driver of gene expression. Whether you are measuring chromatin compaction with ATAC-Seq, Histone PTMs, or other chromatin-associated proteins with ChIP-Seq, Cut&Run, or Cut&Tag, the UMGC can turn your enriched DNA samples into multiplexed libraries ready for Next Generation Sequencing.

Chromatin Profiling Options

ChIP-Seq: ChIP-Seq has historically been the most widely used method of localizing Histone PTMs and chromatin-associated proteins. After crosslinking proteins to the genome and releasing small fragments of DNA from the cell through sonication, factor specific immunoprecipitation is used to enrich for DNA fragments associated with your factor of interest. This workflow has been foundational in our understanding of chromatin structure and gene regulation.

ATAC-Seq: The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility at the genome-wide level. The hyperactive Tn5 transposase inserts sequencing adapters into regions of open chromatin. By sequencing these regions, researchers can investigate areas of increased accessibility and correlate with gene expression. 

Single-cell ATAC-Seq: The Chromium Single Cell ATAC solution provides a robust and scalable approach to mapping the epigenetic landscape at single-cell resolution. By using a transposase enzyme to preferentially tag accessible DNA regions with sequencing adaptors, researchers can now generate sequencing-ready libraries and identify open chromatin regions. Contact

Cut&Run: Cut&Run can accurately map histone post-translational modifications (PTMs) as well as chromatin-associated proteins. Cut&Run relies on an MNase-proteinA/G fusion that can localize MNase DNA cleavage activity to an antibody bound to your factor of interest.  This workflow allows for a much lower background signal than ChIP-Seq because, unlike sonication, the tethered MNase will only release genomic loci physically associated with your factor of interest. Due to this “release specificity,” the cell number and sequence depth required are significantly reduced.

Cut&Tag: While less universally applicable than Cut&Run, Cut&Tag functions well for histone PTMs and feeds into a more streamlined sequencing library prep protocol. Cut&Tag utilizes a Tn5-proteinA/G fusion to tether the Tn5 transposase to an antibody bound to your histone PTM of interest. The tethered Tn5 then inserts a transposon containing sequencing adapters into the adjacent DNA. These resulting DNA fragments can be made into sequencing-ready libraries with a simple PCR.

Start a Project

Contact us a for project support or questions. If your project has unique requirements, higher complexity, or needs optimization, our Custom Services can do non-routine protocols not offered through our Standard Services.


Please inquire about library creation rates at


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How to Order

1. Please contact for project specifications.

2. Once project details are finalized, complete the appropriate submission form for submitting samples or submitting client-made libraries and email to

Illumina Sequencing Request Form (Libraries)

Illumina Sequencing Request Form (Samples)

Shipping Instructions

Samples should be frozen and shipped on dry ice in a 96-well plate. We recommend using plate tape to seal the wells. Place the plate inside of a plastic bag prior to placing on dry ice. Please give advance notice of submission date and time so staff can be prepared to receive samples. If shipping samples from outside the University of Minnesota, ship via express shipping carrier on dry ice to the address below.

Samples can be dropped off at one of our campus locations

1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)

20 Snyder Hall (St. Paul campus)

Samples can be shipped to the following address:

Please send the tracking information to

UMN Genomics Center
ATTN: Elyse Froehling
3510 Hopkins Place N.
Building 4 Suite W402
Oakdale, MN 55128


Data Release

There are four options for transferring data from the UMGC to clients: 1) delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, 2) download from a secure website, 3) download with Globus, or 4) shipment on an external hard drive. Please indicate your data delivery preference when placing an order for sequencing.

1. MSI storage

Internal clients have their data released to MSI's Shared User Resource Facility Storage (SURFS). Delivered data will be located in the "data_delivery" folder in your group's folder on MSI's primary filesystem (home/GROUP/data_delivery/umgc). MSI does not charge for SURFS storage costs, but files expire and are removed one year after they've been delivered. Files should be copied to other MSI storage locations such as Tier2, Tier3, or your group's "shared" folder before they expire. 

2. Web download

Internal clients that opt-out of MSI storage and external clients can download their data from a secure website using either a web browser or a command-line download tool, complete instructions are provided in an email from the UMGC. The client’s data is available for download for 30 days, after which the data will be removed from the data download website and the client takes responsibility for storing the data.

3. Globus

Internal and External clients can use Globus to download their data. This is the recommended method for external clients to download large datasets.

4. Hard drive

External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client at a cost of $250 per hard drive.

Data Recovery

The UMGC archives most customer data for a year and some datasets are retained for 5 years or more. If you need a dataset re-delivered email a request to to initiate data recovery. The UMGC does not provide any guarantee that data can be successfully recovered from the archive.