Service Workflow
This page takes you through the general process for a typical customer to give you an idea of what to expect from our services.
Step 1: Request Services & Schedule Consultation
Contact us at brc_epigenomics@cornell.edu to schedule a consultation and we will assist you in requesting the appropriate services.
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: Wait for Sample Processing
We will process your samples according to our protocols with any changes or details discussed at consultation. Our samples are sequenced in-house on the Element Biosciences AVITI24 short-read sequencer. Sample turnaround time is approximately 2-3 months.
See price list for details on the cost per sample.
Step 4: Accessing Data
Once your samples have been processed, you will receive the following through a Cornell Box link that will be available for 30 days. We keep the meta-information and raw files for you as a part of this service.
- Quality control reports (.html)
- Data summary
- Sequencing files (.fastq)
- BAM alignment files (.bam)
- Strand-Specific BigWig files (.bw) for certain assays
.fastq data and its associated metadata somewhere safe for publication. The other files are for your convenience.- Here are instructions to use Filezilla if you want a GUI interface
- Here are instructions to use the command line
| Service | Raw FASTQ files (R1, R2) | Filtered BAM Alignments | Strand-Specific .bigwig |
|---|---|---|---|
| ChIP-exo | ✔️ | ✔️ | ✔️ |
| ChIP-seq | ✔️ | ✔️ | ✔️ |
| ATAC-seq | ✔️ | ✔️ |
Step 5: Analyzing Data
While performing custom analysis is not a part of our data generation services, we can point you toward resources that might help with your bioinformatics analyses.
There are a number of ways you can analyze your output and many epigenomics analysis resources exist out on the internet.
- Here are recordings of Dr. William KM Lai’s prior epigenomics training sessions. Download materials are available but videos will require BioHPC account login which is free to members of Cornell community.
- For us, the majority of analysis can be done with a flexible graphical interface-based software (ScriptManager) which we recommend to all of our customers.
- Publications from the Pugh Lab or ScriptManager's citation list serve as a rich starting point for sourcing analysis strategies and approaches on ChIP-exo data. If you are working with ATAC-seq or ChIP-seq, the publication landscape is thick with other examples for analyzing your data.
- Please let us know if you would like to schedule a meeting for a consultation on your data and analyses.
Step 6: Publication
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.