The Deep Sequencing Core Facility offers high-throughput sequencing and library-building services for the UMass campuses and outside customers.
Our instruments include the Illumina HiSeq 4000, HiSeq 2000, and MiSeq. Check out the Services page for detailed run options.
**Tickets and forms for sample submission can be found here.**
For a sequencing pricing list, details on specific services, scheduling, or a quote for services, please email us here.
Samples can be left in the labeled fridges at these locations
for 11:00 AM pickup each business day:
Biotech2 outside Suite 207
LRB 6th floor mailroom
We are also available by appointment if you need to visit with us.
Our shipping address for off-campus customers is
Rose-Gordon Bldg. Rm. 141, 222 Maple Ave, Shrewsbury, MA, 01545.
For Illumina Library Building Notes, click here.
Puzzled about Multiplexing and Barcoding? Click here.
There is an updated list of oligo sequences for Illumina library construction. If you are a UMass investigator and wish to obtain a copy, please send an email to Nemo@umassmed.edu and request "the latest Illumina adapter sequences list".
For a letter of support for your grant, click here.
A list of frequently asked questions and answers is here.
The "How Long is THE QUEUE?" FAQ is located here.
We are updating our resources section. If you have a protocol or publication that you found useful, please share. If you have a request for something you think would be beneficial, please email us at DeepSequencingCoreLabs@umassmed.edu.
For those preparing their own libraries, samples should be in ultrapure water or EB. We reserve the choice to hold back a sample which fails QC and contact you to discuss options. The use of a carrier agent during the final stages of workup is discouraged, as these can interfere with cluster formation and reduce the number of reads generated during sequencing.
NOTE: It is VERY IMPORTANT that we receive the correct information about the primers and adapters used to build your library! Not all library types will run on all instruments or can be read in both directions. If you are using the Illumina-style indexes in the TruSeq/Nextera adapters, you must add a multiplex read step to detect your indexes. There is more information in the FAQ and Resources sections. On a related note, if you are doing a custom design to include adapters, your own index scheme, or custom sequencing primers, you must submit the results of your Topo cloning validation before we can run your samples. These sequences must span the P5 and P7 attachment sequences on either end of the library construct. If you do not agree to submit the sequence for verification, then you will be run with only the primers you request and at your own risk.
Please note that a sample submitted for sequencing is entered in the workflow and queue, which engages time and services. If you want the QC analysis only for your own information and are not certain you wish to move forward, please use the MBCL Fragment Analyzer or other QC services (e.g. Topo Cloning, Gel Purification).
Libraries sent for sequencing should have a completed sample ticket (for HS2000/Miseq or for the HS4000) and an Index List form (if applicable). Material sent for library building should ALSO include a library prep ticket. Electronic files are always welcome, especially for long index lists. The Core will accept an email from your PI authorizing charges in liu of a signature.
Finished libraries should be submitted at 10nM concentration in 25u(μ)l of ultrapure water or EB. Please use 1.5mL tubes, 0.5-0.65mL tubes, or PCR strips that are labeled on the top of the tube. Do not submit individual PCR tubes, and avoid long labeling strips that would prevent the tube from fitting in a centrifuge. In the Illumina pipeline, sample names are limited to 20 characters, which can include alphanumerics, "-", or "_".
IF THERE IS A PROBLEM WITH YOUR RUN OR QUESTIONS ABOUT YOUR DATA, please let us know as soon as possible. The run metrics and machine files cannot be held for long because they are extremely large. The sooner we know there is a problem, the more likely we'll be able to help easily. Also, please note that in order to help sort out a problem we may ask a lot of questions and details about your sample and your analysis methods. This information is required in order for us to engage the tech support systems provided by our vendors. Please note that if the control lane on the run failed in any way, the entire flow cell is rerun. If your data is delivered to you, then the controls all passed spec., which means that the instrument functioned properly and the reagents and chemistry worked. That leaves us with investigating other issues including sample design, base balance, sizing, indexing, degraded DNA, as well as computational and analysis issues with the pipeline, etc. We'll do whatever we can to get things working, but the more information we have, the better. We are working on a trouble-shooting guide for libraries; it is under construction and is starting to come together here.
If you would like to consult with an applications specialist, please email us to get on the schedule.
Processing and analyzing a sample requires time and reagents. Payment for these services is the responsibility of the user submitting the sample and should be rendered in a timely fashion. In the event of a reagent or equipment failure, the samples will be rerun at the next possible opportunity at no additional charge.
Clients withdrawing samples prior to the analysis run will be charged a fee to recover QC assay costs. For the return of archived post-analysis samples, clients will be charged a delivery fee per sample.
~~~Inclement Weather Policy~~~
In case of extreme and/or inconvenient weather, the machines will still be running but we
may not be here for sample login or pickup. Please email us to arrange drop-off if the
weather is questionable. The DSCL is closed when UMassMed is on "inclement weather alert“.