PBCE Sample Submission

Material Requirements

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

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 and sample information sheet PER SAMPLE MIX. Electronic files are requested 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 Barcoded M13 or 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 including the barcodes on the sample information sheet.

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

External (non-UMass) customer mandatory information form ( Intake Form )

Supplemental Sheet for PacBio Barcodes/Indexes ( Feb 2023 )

Sequencing Process

The Core Lab staff will QC your submitted sample and enter it in the library prep and sequencing queue. The Core will email you a copy of the QC results upon request. If you then choose not to move forward with library prep/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

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

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 external users get a Globus account. You do not need a full Globus subscription to receive data, however you do need a registered email account. Information about Globus subscription and personal use is available at https://app.globus.org.

If you need an alternative data delivery method, please contact us to discuss it prior to submitting samples.

• Please note:
  
  
• 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. Saving both primary and analyzed data is your responsibility. Please ensure that you safely back your data up!