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Deep Sequencing Services

Core Lab instruments include the Illumina HiSeq 4000, MiSeq, and MiSeqDx.  MiSeq flowcells have a single lane, and their paired-end runs can be customized with asymmetric reads.  (These have a minimum read length of 25bp, and a maximum that depends on the chemistry version. Contact the Core for more info.)  Single or Dual Multiplexing is available on all platforms*.  Some run options are:

Instrument Single Read
Run Length (bp)
Paired-End
Run Length (bp)
HiSeq 4000 50, 100, 150 (4-lane minimum) 50, 100, 150 (4-lane minimum), special 50x100 for Chromium 10X (phiX required)
MiSeq and MiSeqDx 50, 100, 150
(Contact us for pricing and availability if you need a read length not listed.)
25, 100, 150, 250, 300, asymmetric

If you are unsure about which instrument or run type you want, we recommend contacting the Core to discuss your project needs with Core Lab staff.

Sequencing results from all Core Lab instruments are intended for research purposes only.

Library Construction
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Library construction services provided by the Core include conversion of DNA or RNA into ligated & indexed Illumina libraries, size-selection, and QC by Fragment Analyzer and/or any other means necessary. Please go here for more information or email Maria.Zapp@umassmed.edu to discuss your project. The library prep ticket can be found in the Documents section below.

Indexing
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Indexed (aka multiplexed) libraries can be mixed together and run in a single lane if you do not need the maximum amount of depth available. "Illumina-style" indexes are located between the P7 or P5 linker and associated adapter, and require a separate read. "Inline barcodes", on the other hand, are read as part of your insert (not an index read), and require base-balancing.

     *Single and Dual Multiplexing are distinct from Single and Paired-End reads. Single multiplexed libraries have an index (called i7) at the P7 end, while dual multiplexed libraries have indexes at BOTH the P7 and P5 ends (i7 and i5). Each index that is placed in an adapter requires a separate read that is distinct from any insert reads, so Paired-End runs can have Single Indexing, and Single-Read runs can use Dual Indexing. The Core will demultiplex your libraries after the run provided that you send a list of sample names and indexes. For more details on multiplexing, click here.

Downloadable Documents
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HiSeq/MiSeq Analysis Order Form ( Jul 2019 ) ( fillable pdf )

Supplemental Sheet for Index List ( Jul 2017 )

Library Construction Order Form ( Apr 2020 ) ( fillable pdf )

Sample Submission Instructions ( click here )

DSCL workflow diagram ( click here )

Ticket Example With Tips ( example sheet )

Equipment at the Core
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A list of the equipment owned by the Core can be found here. The equipment is not available for general use, but if you need it and it is not listed as a Core Service, you can email DeepSequencingCoreLabs@umassmed.edu to discuss the possibility of a custom service from the Core.

Pricing and Payment Policy
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Please email DeepSequencingCoreLabs@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 or pickup. Please email us to arrange drop-off if the weather is questionable. The DSCL, MBCL, & PBCE are closed when UMassMed is on "inclement weather alert“.

UMMS PacBio Core logo linking to website

UMMS Molecular Biology Core Labs logo linking to website