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PBCE Sample Submission


Material Requirements
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If you are new to PacBio Sequencing, see the Resources section for basic information and helpful links.

Please fill out the service ticket(s) as completely and accurately as you can. Submitted material should be high-quality, clean, and contaminant-free, in EB or water.

Sample Submission Process
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Please email the PBCE to request the most recent version of our service ticket.

Material should be submitted at the requested concentration listed on the service ticket for your desired library type. Amplicons should be in 15-20 ul of EB or water, and genomic material is preferred in 15-50 ul of EB or water. The outcome of libraries made from material submitted below the requested concentration and quality standards may not be guaranteed by the Core.

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 single PCR tubes, and avoid long labeling strips that would prevent the tube(s) from fitting in a centrifuge.

In the data pipeline, characters used for sample names are limited to alphanumerics, "-", or "_".

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 methods (e.g. Topo Cloning, Gel Purification).

Material sent for sequencing should have one completed ticket PER SAMPLE MIX, and an Index List form if applicable. Electronic files are always welcome in addition to paper tickets. For internal UMass customers, the Core will accept an email from your PI authorizing charges in lieu of a signature. External customers must complete a Customer Intake Form in addition to the service ticket.
Typically we suggest that you send indexed libraries separately and let us do the mixing by molarity based on our internal QC. This helps with any potential troubleshooting if some samples in the mix underperform. However, if you prefer to premix your samples or choose a different mixing method (such as by volume), you are welcome to.

The PBCE can demultiplex your library mix after the run if you have used PacBio internal barcode sequences such as the Barcodes Universal F/R Primers or if indexed adapters are used to build the library. If this applies to you, please inform us by filling out the relevant section on the service ticket and sending us a list of sample names vs. barcodes.

Drop-off locations:
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
AS8-2016
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.

Downloadable Forms and Documents
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External (non-UMass) customer mandatory information form ( Intake Form )

Supplemental Sheet for PacBio Barcodes/Indexes ( Sep 2021 )

Sequencing Process
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The Core Lab staff will QC your submitted sample and enter it in the queue. The Core will email you a copy of the QC results upon request. If you then choose not to move forward with sequencing, the Core will bill for the QC and processing to recoup costs. Samples will be processed on a first-come, first-served basis.

Data Analysis
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After the data collection is complete, samples enter the bioinformatics pipeline. The time required to complete this varies based on the analyses requested as well as the state of the High Performance Computing Cluster.

If you intend to do additional analyses of your own, please see the Data and Bioinformatics section for information. If you would like to consult with an applications specialist, please email us to get on the schedule.

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. 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 library on the run failed in any way, the SMRTcell is rerun. If your data is delivered to you, then the controls all passed spec., which means that the instrument, reagents, and chemistry functioned properly. That leaves us with investigating other issues including sample design, 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.

Data Transfer
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You will receive an email notification when your data is ready. Instructions on how to retrieve your data will be included in the email.

The amount of data generated from a sequencing run can be extremely large. We recommend eligible users get an account on the Green High Performance Computing Cluster for data delivery. See this WIKI for more information. To get an account, contact the UMassMed Help Desk at 856 - 8643, email them at hpcc-support@umassmed.edu, or request access through this form.

Alternatives for non-UMass customers are to have the data uploaded to an outside server (using SFTP) or transferred to an external drive meeting our requirements and shipped overnight.

  • Our current GHPCC data delivery system:
    (note that this changes as resources improve/upgrade, so stay tuned)

    • Your lab will have a directory at /project/umw_deepseq/FOR_DELIVERY/
    • You will get an email notification when your data files are ready.
    • Data files will be deleted 5 business days after notification; please backup/copy/archive your data in your own workspace.
    • The PBCE does not have the resources to archive or recover data. Please ensure that you safely back your data up!

Pricing and Payment Policy
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Please email PacBio@umassmed.edu to get a quote for your desired services.

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
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In case of extreme and/or inconvenient weather, the machines will still be running but we may not be here for sample login, pickup, or delivery. Please email us to arrange drop-off if the weather is questionable. The PBCE, DSCL, & MBCL are closed when UMassMed is on "inclement weather alert".

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