Deep Sequencing Core Facility

The Pacific BioSciences RS Instrument is here and running samples !

The Website for the new PacBio Enterprise is under construction ...

We have 3 drop off locations and we are available by appointment.
Drop off sites are Biotech2 Suite 207 hallway, LRB 6th floor mailroom, and ASC8-2058 mailroom, the daily pick up is after 11:00 am each business day.
We can meet you by appointment if you need to visit with us.
Thank you, The DSCL Staff   

Please use the newest Sample Ticket (Dec 2013b) for all DeepSeq samples, including HiSeq & MiSeq. Submitting a sample and a ticket begins a workflow for your sample and reserves a place in the queue. By submitting a sample and ticket, you are engaging time and services.  If you want only the QC analysis for your own information and do not want to move forward, please use the MBCL Bioanalyzer and QC services (e.g. Topo Cloning, Gel Purification and Library Construction). We reserve the option of holding back a sample which fails QC and contacting you to discuss options. However, please note that a sample submitted for sequencing is entered in the workflow and queue.  For those preparing their own libraries, samples should be in ultra pure water or EB. The use of a carrier agent during the final stages of work up is discouraged as these can interfere with cluster formation and reduce the number of sequences produced during "deep sequencing". For a pricing list or other HiSeq questions, please email us.

The UMass MBCL is now building genomic DNA libraries for HiSeq analysis.
email us to inquire about scheduling, etc.!

We are now operating an Illumina MiSeq instrument. This platform supports dual indexes and will perform paired reads up to 300 bases.
Please email us for more information. 

Illumina Library Building Notes click here

If you'd like details on specific services or a quote for services, please click here.

There is an updated list of sequences for Illumina library construction. If you are UMass investigator and wish to obtain a copy, please send an email to NEMO@umassmed.edu and request "the new oligo list".

For a letter of support for your grant, click here

"How Long is THE QUEUE" FAQ is here

A list of frequently asked questions and some answers are here
Puzzled about Multiplexing and Barcoding? Click Here.

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 the HiSeq instruments or can be read in both directions. If you are using the Illumina internal barcodes in the TruSeq adapaters, you must add a multiplex read step to detect your barcodes. There is more information in the FAQ. 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.

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 since they are 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 alot of questions and details about your sample and your analysis methods. This information is required inorder 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.

We are building a new 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 let us know, email us at DeepSequencingCoreLabs@umassmed.edu

If you would like to consult with an applications specialist, please email us to get on the schedule.

Link to BioTools for Next Gen Sequencing Documents click here
Information about NextGen BioInformatics Tools on HPCC click here

New Tool for Data Quality Score Viewing FASTQC

Payment Policy:  Processing and analyzing a sample requires time and reagents. Payment for these services is the responsibility of the user submitting the sample. In the event of a reagent or equipment failure, the samples will be rerun at the next possible opportunity at no additional charge.

WEATHER ALERT ~ ~ ~ In case of extreme and/or inconvenient weather, the machines will still be running but we may not be here for sample login. Please email us to arrange drop off if the weather is questionable. 

These results are intended for research use only, and are not appropriate for use in clinical diagnosis nor for forensic purposes.


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