UMass Boston

Sequencing Services

- 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).

Library Preparation Services

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. 

The core 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.

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.