Skip to main content

Cornell University

Service Workflow

Step 1: Request Services & Schedule Consultation

Step 2: Submit Samples

After discussing projects during the free consultation and by email, researchers will email us their sample submission form (SSF). Sample drop off should be scheduled by email for delivery on dry ice either in person in Biotech 467, on the C2C bus (Weill Cornell only), or shipped as described below. All samples are photographed and documented upon arrival.  

Shipping Instructions

Take a picture of the tubes so that their labels are visible
Please check that tube labels and order agree with the forms you have submitted and are legible in the photo.
Ship samples in dry ice, and if you include your own antibody, ship the antibody on ice.
Include a sample tube with plain ice to verify temperature integrity during transit.
Deliver or send samples via express mail to:
    Cornell Epigenomics Core (EGC)
    526 Campus Road
    467 Biotech Bldg
    Ithaca, NY 14853

Step 3: Process Samples

Step 4: Access Data

  • -Sample turnaround time is approximately 2-3 months
  • -Quality control reports are provided, along with a data summary
  • -Sequencing files and QC report are provided via Box link
  • -Cite us! All presentations and publications including this data should acknowledge the Cornell BRC Epigenomics Facility and include our facility RRID (RRID:SCR_021287). Thanks!

Datafiles & Analysis

We provide the raw FastQ files, raw BAMs, filtered BAMs, and strand-specific bigWig files from the sequencing results to you together with a copy of this summary report. The files are available in a shared Cornell Box folder for 30 days. An invitation to join the Box folder will be sent to you. We keep the metainformation and raw files for you as a part of this service.

Dr. Will Lai has developed a GUI interface for some standard approaches to analyzing ChIP-exo data. You can download the software from his repo – https://github.com/CEGRcode/scriptmanager.

Data Management and Sharing

Our services rely upon the Platform for Eukaryotic Genomic Regulation (PEGR RRID:SCR_021861), an open-source tracking system for ChIP-exo, ATAC-seq, ChIP-seq and other assays. PEGR is integrated with our lab’s implementation of NSF/NIH funded Galaxy.org for FAIR compliant, rigorous workflows that generate entirely reproducible datasets that we provide and host for our researchers. Our entire suite of open-source software platforms together provide end-to-end tracking of sample preparation from NGS sequencing to generation of publication-quality figures that are intrinsically linked to the meta-information available in each step of the sample experiment. Our software is designed to be accessible to biochemists and clinicians who may be less familiar with Epigenomics research, allowing researchers to aggregate samples and combine the results over thousands of datasets.

The PEGR platform, integrated with our Galaxy.org workflow engines and our own STENCIL (RRID:SCR_021878) visualization application, has been deployed in experimental work for over five years and enabled the following large-scale NIH funded projects:

Further development is ongoing to leverage government-funded cloud services available through Cornell’s involvement with Jetstream2, XSEDE and OSG to enable practically unlimited free access to nationally funded supercomputing systems for processing our researcher workflows. We also intend to extend our Epigenomics assays and services to include additional methods for technical processing of tissue and cell samples.

Our software platforms, including PEGR, were developed in collaboration with Frank Pugh, professor in the department of Molecular Biology and Genetics at Cornell; William KM Lai, Assistant Research Professor in the departments of Molecular Biology and Genetics and Department of Computational Biology at Cornell; Shaun Mahony, Associate Professor in the Biochemistry & Molecular Biology Department at Penn State University, and the Galaxy.org team at Penn State.To learn more about what we do and how it could further your research aims, contact us at brc_epigenomics@cornell.edu. We are looking forward to enabling exciting scientific discoveries together.

Step 5: Finish Up

Acknowledging EGC services

If you publish data that has been generated with the help of the services we provide, mentioning the Cornell Institute of Biotechnology in the acknowledgments section is very helpful. Here is why. You can also review our authorship guidelines.

To cite us is simple, just put (Cornell University BRC Epigenomics Core Facility, RRID:SCR_021287) in your acknowledgements.