Deep Sequencing Services

HiSeq instrument     Core Lab instruments include the Illumina HiSeq 4000, HiSeq 2000, and MiSeq.  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:

Single Read
Run Length
Run Length
HiSeq2000 50, 100 50, 100
HiSeq4000 50, 100, 150 (4-lane minimum) 50, 100, 150 (4-lane minimum)
MiSeq 50, 100, 150 25, 100, 150, 250, 300, asymmetric

     Library construction services from the MBCL include conversion of DNA or RNA into ligated & indexed Illumina libraries, size-selection, and QC by Fragment Analyzer and/or any other means necessary.

     *Single and Dual Multiplexing are distinct from Single and Paired-End reads. Each index that is placed in an adapter requires a separate read, so paired-end runs can have single-end 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. Inline barcodes are read as part of your insert (not an index read), and require base-balancing. For more details on multiplexing, click here.

     Libraries should be submitted at 10nM concentration in 25ul of ultrapure water or EB. 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 individual PCR tubes, and avoid long labeling strips that would prevent the tube from fitting in a centrifuge. In the Illumina pipeline, sample names are limited to 20 characters, which can include alphanumerics, "-", or "_".

HS2000/MiSeq Analysis Order Form ( Aug 2015 ) ( fillable pdf )
HS4000 Analysis Order Form ( Aug 2015 ) ( fillable pdf )
Supplemental Sheet for Index List ( Jul 2017 )
Library Construction Order Form ( Aug 2017 ) ( fillable pdf )
Sample Submission Instructions ( click here )

Illumina TruSeq Prep GuidesNautilis symbol

    TruSeq RNA ( click here )
    TruSeq Small RNA ( click here )
    TruSeq DNA ( click here )

Chromatin IP Library Protocols

    Illumina Chromatin IP ( click here )
    Newer Illumina ChIP Seq Prep ( click here )
    Data Sheet ( Data Sheet )

    Core Lab Notes ( click here )

Genomic DNA Library Protocols 

    Illumina Genomic DNA ( click here )
    Core Lab Notes ( click here )

Small RNA Library Protocols

    Illumina Small RNA Protocol NEW ( click here )
    Illumina Small RNA ( click here )
    Mello Lab small RNA ( click here )
    NEW and IMPROVED 14 JULY Mello Lab small RNA ( click here )

Expression/cDNA libraries

    Illumina Protocols (long) available from core lab, please email to request them. (Why "Nemo"?)

~~~Inclement Weather Policy~~~
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 is closed when UMassMed is on "inclement weather alert“.
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