MBCL IDT Portal
Deep Sequencing Services
DSCL instruments include the Illumina NovaSeq 6000, 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 (see section below).
Current Run Options
| Instrument | Single Read Run Length (bp) |
Paired-End Run Length (bp) |
|---|---|---|
| NovaSeq 6000 | SR 100 | PE 50 x 50 PE 100 x 100 PE for Chromium 10X (<=138 cycles) PE 150 x 150 (whole flowcell only) |
| MiSeq and MiSeqDx | SR 50 SR 100 SR 150 (Contact us for pricing and availability of read lengths not listed.) |
PE 25 x 25 PE 100 x 100 PE 150 x 150 PE 250 x 250 PE 300 x 300 Asymmetric (min. 25 bases each read) |
If you are unsure about which instrument or run type you want, we recommend contacting the Core to discuss your project needs.
Sequencing results from all Core Lab instruments are intended for research purposes only.
Library Construction
Library construction services provided by the Core (through the MBCL) include:
- Conversion of DNA, RNA, or cells into ligated & indexed Illumina libraries
- Library prep from NanoString GeoMx plates
- Size-selection
- QC by Fragment Analyzer and/or any other means necessary
Please go to the MBCL's Library Prep Service page for more information or email Maria.Zapp@umassmed.edu to discuss your project. The library prep ticket can be found in the Documents section of the Sample Submission page.
Indexing
Indexed/multiplexed/barcoded libraries can be mixed and run together 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.
For very high-throughput instruments like the NovaSeq, dual 8bp indexing or better is strongly recommended. See the Sample Submission and Resources pages for more details about library structure.
The Core will demultiplex your libraries after the run provided that you send a list of sample names and indexes.
Equipment at the Core
Here is a list of the equipment owned by the Core. The equipment is not available for walk-ins or scheduled general use. If you need something not offered as a Core service, please email DeepSequencingCoreLabs@umassmed.edu to discuss the possibility of a custom service.
Pricing and Payment Policy
Please email DeepSequencingCoreLabs@umassmed.edu to get a quote for your desired services.
Processing and analyzing a sample requires time and reagents. Payment for services is the responsibility of the user submitting the sample and should be rendered in a timely fashion. In the event of reagent or equipment failure, samples will be rerun at the next possible opportunity with 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.
A signed ticket or email authorization indicates that the holder of the listed account consents to payment in accordance with this policy.
Inclement Weather Policy
In case of extreme weather or campus closures, the machines will be operating but we may not conduct a sample pickup. Please email us to arrange for sample drop-off if the weather is questionable. The DSCL, MBCL, & PBCE are closed when UMass Chan is on "inclement weather alert".
MBCL IDT Portal