UMass Boston

• Xenium is here! Take a look at the new 10X Genomics platform and Core services designed to explore your tissue with 5,000 genes to deeply characterize cell types, pathways, cell-cell interactions & more.
• Sequencing just got cheaper with XLEAP reagents from Illumina! Our pricing decreased from 10-28%, with an average 16% reduction in costs. Check it out in the Pricing and iLab Solutions section! 

Please cite the use of the Center for Personalized Cancer Therapy Genomics Core and its grant support as part of the NIH/NCI U54 CA156734 award Shared Resources Core in your papers and presentations. Thank you!

10X Genomics Single Cell Sequencing

Custom run parameters for Single Cell Sequencing using the 10X Chromium platform is also available (rates available in iLabs)

Illumina NextSeq 2000

The Illumina NextSeq 2000 System is a powerful and efficient high-throughput sequencing system that supports a range of applications and study sizes.  Our new sequencer supports massively parallel sequencing using Sequence By Synthesis (SBS) technology that detects single bases as they are incorporated into growing DNA strands.  Multiple flow cell configurations enable economical and high throughput sequencing output of 40-330 Gb per run, providing adjustable output based on project needs, with a lower carbon footprint.  Single or paired end sequencing compatible. Maximum output of 120 Gb (with P2 reagents), 330 Gb (with P3 reagents), and Maximum Reads per Run up to 400M single reads (with P2 reagents), and 1.1 billion single reads (with P3 reagents).

Our NGS library prep and sequencing service includes preparation of libraries from DNA, RNA, or single cell suspensions.  These services include library preparation, QC, and pooling of samples followed by sequencing on the Illumina HiSeq 2500 v4 or Illumina Miseq instruments.

DNA-Seq Library Prep

The KAPA Hyper Prep Kit is a robust, streamlined solution for DNA library preparation for Illumina sequencing.  The chemistry has been optimized to produce higher yields of adapter-ligated library and lower amplification bias.  This results in increased diversity, lower duplication rates and more uniform coverage.  It is compatible with FFPE and low-input samples.  Our DNA-Seq library construction is performed on a Beckman Biomek FXp Laboratory Automation Workstation.

Low Input DNA-Seq

The NEBNext Ultra II DNA Library Prep kit utilizes a novel enzymatic cocktail to allow one-step fragmentation, end-repair and a-tailing, which reduces transfers and cleanups to minimize sample loss.  This protocol allows for construction of libraries from as little as 100pg of input DNA.

Metagenomic Libraries

The Bioo NEXTflex 16s Amplicon-seq 2.0 kit targets v1-3 or v4 hypervariable regions of the 16s ribosomal gene to prepare libraries for Miseq sequencing to characterize microbial communities.  Please contact us to choose the best primer set for your study.

RNA-Seq Library Prep

The KAPA Stranded RNA-Seq kit with RiboErase produces high-quality RNA libraries for Illumina platforms.  The kit includes KAPA HiFi enzyme for high-efficiency and low-bias library amplification, and includes a streamlined, “with-bead” protocol.  We also offer the KAPA Stranded RNA-Seq kit with Poly-A capture, for mRNA only libraries depending on study design.

Small RNA Libraries

The NEXTflex Small RNA v3 preparation offers a gel-free small RNA protocol with randomized adapters to reduce ligation bias for sequencing of miRNA and other small RNA species.

Single Cell Library Prep

The 10X Genomics Chromium Controller allows construction of Illumina-compatible libraries from cell suspensions for single-cell resolution in gene expression, immune profiling, or ATAC-seq studies. 

Libraries Constructed in Your Lab

The core facility is also equipped to process libraries you have constructed in your own lab.  We will perform QC assays (Qubit, Bioanalyzer and KAPA qPCR quantitation), pool your samples and sequence them on the HiSeq 2500 v4 instrument.

The Genomics Core is now providing some in-house bioinfomatics services with plans to expand offerings over the coming months!  Please contact us  to schedule a consultation.  We have also partnered with GeneVia,  which offers Genomics Core users a 10% discount on analysis of genomic data:

Download GeneVia Brochure

For custom bioinformatics analysis, we have a partnership with Genevia Technologies. All customers of our core services are eligible for a flat 10% discount on data analysis projects. 

Learn more about Genevia’s service model from this video.

Learn more about Genevia’s offerings and references in cancer research.

GeneVia RNA-Seq Bioinformatics grant opportunity! 

The following equipment is available through the Genomics Core Facility.

Agilent 2100 Bioanalyzer

The Agilent 2100 Bioanalyzer is a microfluidics-based platform that provides sizing, quantification and quality control of nucleic acids. 

DNA High Sensitivity Chip

DNA 1000 Chip

RNA 6000 Pico Chip

RNA 6000 Nano Chip

Agilent 2200 Tapestation

The Agilent 2200 Tapestation system automates RNA and DNA sample QC.  Separation and analysis of nucleic acid is carried out with only 1 ul of material.

              DNA 1000 Assay

              RNA Assay

QUBIT

The Qubit 2.0 fluorometer accurately quantifies DNA and RNA.  It provides a very sensitive assay as the fluorescent dyes bind only to the target molecule.  As little as 1 ul of sample can be used for each measurement.  The Qubit does not provide 260/280 or 260/230 ratios.

              DNA Broad Assay

              DNA High Sensitivity Assay

              RNA Broad Assay

              RNA High Sensitivity Assay

Nanodrop Lite

The Nanodrop Lite is a UV spectrophotometer designed for quantitation of nucleic acids using microvolumes of sample.  Concentration is measured at 260 nm and purity is determined using the 260/280 ratio. 

Shearing Services

The Covaris S220 uses Adaptive Focused Acoustics™ (AFA) to shear DNA for next generation sequencing library applications.  The AFA delivers high frequency ultrasonic energy to process samples in a non-contact environment.

Nanostring nCOUNTER Analysis System

The Nanostring nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 unique molecules simultaneously from a single sample in a single reaction using a novel barcoding technology.  Each fluorescently labeled barcode is attached to a single target-specific probe corresponding to a gene of interest.  Mixed together with controls, the probes form a multiplexed CodeSet.

Visit nanoString for available panels.           

Nanostring also offers Custom CodeSet Design.  This is available to assay any target sequences for any organism.  All custom CodeSets undergo extensive quality-control testing before they are delivered.  Contact us and we will put you in touch with a design expert.

QuantStudio™ 12K Flex Real-Time PCR System

The QuantStudio 12K Flex RealTime PCR System workflow includes real-time thermal cycling and fluorescent data collection from TaqMan Assays.  The instrument is equipped to process 384 well plates.

For current pricing, please create an iLabs Account. It's easy! You just need your institutional email and create a password. There is no marketing or private information associated with your iLabs account. Please follow the steps below.

Create an iLabs Account

Log Into iLabs

The Genomics Core at the University of Massachusetts Boston uses an online system to streamline the process of requesting and billing for core services.  After you create an iLab account, the system will enable you to view pricing, place service requests, provide required approvals, enter your fund or PO number, complete and print submission forms to accompany your samples and track whether your submission has been received, started or completed.

If you experience any problems using iLab, click the 'leave iLab feedback' link in the upper right hand corner once you are logged in.  Alternatively, send an email to support@ilabsolutions.com or call 617-297-2805.

If you are a new Principal Investigator, see below for instructions.

If you already have an iLab account:

• Please click the 'Log Into iLab' button top of page.
• For those who have an existing iLab account but need a password.

New Users:  To register for an iLab account:

1. Click the 'Create an iLab Account' button above.
2. Complete the registration form on the sign-up page.  Use your institutional email.
3. Receive a Welcome Email from iLab (typically within one business day) with login credentials.

To Create a Service Request:

1. Obtain your Fund or PO number to be entered with your request.
2. Login Here
3. Enter the credentials received in your welcome email from iLab.
4. Select the Request Services tab and click on the Request Service button next to the service of interest.
5. You will be asked to complete a form.
6. Your request will be pending review by the core.  The core will review and/or add charges and submit it back to you for approval.  Make sure to watch for an email from iLab regarding your updated project and be sure to provide payment information for your request before agreeing to the quote.

To Create an Equipment Reservation for the QuantStudio™ or Computer Workstation:

1. Obtain your fund or PO number to be entered with your request.
2. Login Here
3. Enter the credentials received in your welcome email from iLab.
4. Select the Schedule Equipment tab and click on the View Schedule button next to the instrument of interest.  Click and drag on the time frame you would like to schedule your reservation for.
5. A window will pop up that will allow you to verify your reservations details and provide payment information before saving the reservation.
6. Your reservation may need to be approved by the core.  You can confirm this by viewing your homepage (click the “Home” button in the upper left corner of the iLab window).

For any questions not addressed in the manual, click on the “leave iLab feedback” link in the upper right hand corner or contact support@ilabsolutions.com.

For Principal Investigators:

Each of your lab members will have to request permission to be a part of your lab before they are able to place orders.  You will receive notification when someone is requesting permission.  The request email will have specific instructions on how to approve the request.  In case you are interested in the process, we have pasted instructions below.  If you would prefer to delegate these notifications/approvals to a financial manager, please email support@ilabsolutions.com with your financial manager’s name & email.

Instructions:

1. iLabSolutions Service Center Assistance
2. You will use your User id and password to log into iLab.
3. Once logged in, look for the link in the left hand menu that says 'my labs'. Hover-over and select your lab.
4. Set the auto-approval amount if you do not wish to approve service requests below a certain dollar amount.  To do this, select the 'Members' panel and enter a dollar amount in the 'Auto Pre-Approval' amount and click 'save settings.’
5. To approve lab membership requests, select the ‘Membership Requests & Fund Numbers’ tab. New membership requests will show at the top of this page.  Click “Approve” to accept a member into your lab. Click “Reject” if they are not a member of your lab.
6. To assign a Fund Number to a member of your lab, find the member in the above list where it says, ‘Manage Fund Numbers’ Select the checkbox(es) to the right of their name for the Fund Number(s) you wish to assign them.

Additional Help

For any questions not addressed in the manual, click on the “leave iLab feedback” link in the upper right hand corner of the iLab page or contact support@ilabsolutions.com.