Epigenomics Core
Claudia Lalancette in the Epigenomics Lab

Preparing samples for analysis in epigenetic regulation in both genome-wide and locus-specific manners.

Project Request

The Epigenomics Core provides resources and services to prepare samples for analysis in epigenetic regulation in both genome-wide and locus-specific manners. Epigenetic regulation refers to DNA sequence-independent regulation of heritable traits that impacts gene expression. In recent years the term has broadened to also encompass processes that control gene expression and genomic functions beyond DNA sequence but which may be more transient or facultative in nature.

Our Process
Project Initiation

Investigator submits a project request.

Submit Samples

After consultation with our team, the investigator delivers samples to us for review.

Sample Processing

We'll oversee the quality control of samples, providing assay-specific sample processing and library preparation. We then submit to the Advanced Genomics Core for processing.

Data Review

Our team reviews the resulting data from the Advanced Genomics Core, providing quality control, alignment, and analysis.

How we Serve Your Research Needs
Equipment in the Epigenomics Core
Chromatin Conformation

providing information on the 3D organization of the genome and its role in gene regulation

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Equipment in the Epigenomics Core
Cytosine Modifications

providing information on DNA methylation status across the genome at different levels of resolution

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Equipment in the Epigenomics Core
Histone Modifications

mapping genome-wide distribution patterns of specific histone modifications

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Project Request
Equipment in the Epigenomics Core
Chromatin Accessibility

identifying accessible regions in the chromatin structure

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Our Rates
Service RequestedUnitInternal Rate (U-M
Sample Quality Control only (Qubit and TapeStation)per sample$28
Sample Quality Control and Bisulfite Treatmentper sample$34
PCR Reaction (includes QC on TapeStation)per sample$29
DNA Extraction & Quality Controlper sample$40
Cryopulverization of flash frozen tissues (materials + labor)per sample$52
nuclei preparation from flash frozen tissues (includes cryopulverization material and labor)per sample$78
nuclei preparation from fresh or cryopreserved cells (materials + labor)per sample$46
Service RequestedUnitInternal Rate (U-M)
WGBS (includes sample QC and library QC/quant)per assay$277
mERRBS (includes sample QC and library QC/quant)per assay$267
ChIP-seq library (includes sample QC and library QC/quant)per assay$212
ATAC-Seq library prep (includes library QC/quant; nuclei prep depends on material)per assay$236
Amplicon Bisulfite-Seq library preparation (library QC/quant)per assay$90
5hMeDIP-Seq (includes sample QC and library QC/quant)per sample$235
Sample Preparation Labor Rateper hour$121
Pyrosequencingfull plate$363
OxBS-Seq Preparationper samplecontact us

Please Note: Sequencing costs are based on Advanced Genomics Core rates.

NovaSeq 6000UnitInternal Rate (U-M)
Illumina NovaSeq 6000 (SP) 100 Cycle Sequencingper flow cell$3,972
Illumina NovaSeq 6000 (SP) 300 Cycle Sequencingper flow cell$4,973
Illumina NovaSeq 6000 (SP) 500 Cycle Sequencingper flow cell$6,309
Illumina NovaSeq 6000 (S1) 100 Cycle Sequencingper flow cell$6,292
Illumina NovaSeq 6000 (S1) 200 Cycle Sequencingper flow cell$7,405
Illumina NovaSeq 6000 (S1) 300 Cycle Sequencingper flow cell$7,850
Illumina NovaSeq 6000 (S2) 100 Cycle Sequencingper flow cell$10,471
Illumina NovaSeq 6000 (S2) 200 Cycle Sequencingper flow cell$12,418
Illumina NovaSeq 6000 (S2) 300 Cycle Sequencingper flow cell$13,086
Illumina NovaSeq 6000 (S4) 200 Cycle Sequencingper flow cell$18,476
Illumina NovaSeq 6000 (S4) 300 Cycle Sequencingper flow cell$20,408

One array requires 16 samples. Cost is greater if fewer than 16 hybridizations are requested. For pricing please contact [email protected].

What to Expect When You Work with Us

Included in the service request to the Epigenomics Core is the following output:

  • Raw sequence data (FASTQ files)
  • FASTCQ output (HTML and TXT files)

For ERRBS/mERRBS and WGBS projects the following files are also provided:

  • CpG context methylation calls (TXT files)
  • CpG context methylation calls for visualization (BEDGRAPH files)
  • Summary statistics (Excel file)

For a more in-depth analysis, or if you require custom output, please state your interest at the consultation.

Publications
Authors Year Publication
Straight, B, Fisher, G, Needham, BL, Naugle A, Olungah C, Wanitjirattikal P, Root C, Farman J, Barkman T, Lalancette C. 2019 Lifetime stress and war exposure timing may predict methylation changes at NR3C1 based on a pilot study in a warrior cohort in a small‐scale society in Kenya. Am J Hum Biol. 2020; e23515.
Huber AK, Patel N, Pagani CA, Marini S, Padmanabhan KR, Matera DL, Said M, Hwang C, Hsu GC-Y, Poli AA, Strong AL, Visser ND, Greenstein JA, Nelson R, Li S, Longaker MT, Tang Y, Weiss SJ, Baker BM, James AW, Levi B. 2019 Immobilization after injury alters extracellular matrix and stem cell fate. Published October 1, 2020; First published July 16, 2020, J Clin Invest. 2020; 130(10): 5444-5460.

Acknowledgment of Contributions

Projects that use data or samples generated by the Epigenomics Core and result in publication should include an acknowledgement of the Core or include members as coauthors. The Epigenomics Core uses these acknowledgements and authorship to help demonstrate our contributions to the research community. This in turn helps secure future funding to maintain a robust Core facility and provide professional development of its staff. The Association of Biomolecular Resource Facilities has published a guideline to use when considering whether or not to include core laboratory members on publications.

Our Leadership
Dana Dolinoy Dana Dolinoy, Ph.D.
Faculty Director
Claudia Lalancette Claudia Lalancette, Ph.D.
Managing Director
Questions?
Contact Us
Room C568
Medical Science Research Building (MSRB) II
1150 West Medical Center Drive
Ann Arbor, MI 48109
Phone: 734-764-2223
About Us
The Epigenomics Core is one of the Biomedical Research Core Facilities, and a part of the Medical School Office of Research, where our mission is to foster an environment of innovation and efficiency that serves the Michigan Medicine research community and supports biomedical science from insight to impact.
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