The University of Massachusetts Amherst
Illumina MiSeq Sequencing System

Genomics Resource Laboratory

Located on the 3rd floor in the Morrill Science Center the Genomics Resource Laboratory (GRL) provides services and advanced instrumentation support for nucleic acid (DNA and RNA) analysis.

The GRL provides a suite of services to address your high-throughput next-generation sequencing, including solutions for sample processing such as nucleic-acid isolation, nucleic-acid quantitative and qualitative analysis, NGS library preparation, quantitative-PCR analysis, etc.

We provide a sample processing and library preparation such as whole genome sequencing, shotgun metagenomics, metatranscriptomics, targeted amplicon sequencing, RNA-Seq, ChIP-Seq, Exome Sequencing, Methyl-seq, Single Cell Genomics, etc., to address your NGS projects.

The facility accepts samples and will perform requested analysis. We offer training to users to conduct experimentation for use on a fee for service basis to both internal and external researchers, academic or industry based.

Following an initial consultation, covering experimental parameters training and access is arranged through the director.

What Makes Us Unique

  • Library preparation
    • Whole genome sequencing
    • Shotgun metagenomics
    • Metatranscriptomics
    • 16S/18S rRNA amplicon library prep
    • RNA-Seq
    • ChIP-Seq
    • Other library preps
  • DNA and RNA isolation
  • Illumina NextSeq 500 Sequencing System

    High-throughput sequencer with quick turnaround time, capable of generating up to 120 Gb data, with 800 million paired-end sequencing reads and 150 bp read length. Used for large whole genome sequencing projects, Methyl-Seq, RNA-Seq, exome sequencing projects, etc.

    illumina.com

  • Illumina MiSeq Sequencing System

    Mid-throughput sequencer, capable of generating up to 15 Gb data with 50 million paired-end sequencing reads with 300 bp read length. Applied for applications such as 16S rRNA amplicon sequencing, targeted gene sequencing, small genome sequencing and targeted gene expression.

    illumina.com

  • Fluidigm C1 Single-Cell Auto Prep System

    The innovative C1 system carefully isolates single cells into individual reaction chambers in the exclusive Fluidigm integrated fluidic circuit (IFC). The optically clear IFC lets you automatically stain captured cells and examine them by microscopy for viability, surface markers or reporter genes. After staining, cells are automatically lysed and template is quickly prepared for qPCR or sequencing analysis—all in as little as four hours.

    fluidigm.com

  • Bioruptor Pico Sonicator System

    Sonication device for shearing DNA and RNA for NGS applications. Optimized for volumes of 20 - 100 μl.

    diagenode.com

  • BluePippin, Sage Science

    DNA size selection system, capable of selecting to 100 bp – 50 kb for NGS applications. Has integrated pulsed-field electrophoresis for resolving and collecting high molecular weight DNA for PacBio library prep as well.

    sagescience.com

  • Agilent 2100 Bioanalyzer

    Used for sizing, quantitation and quality control of DNA, RNA, and proteins.

    genomics.agilent.com

  • FastPrep-24 5G Sample Homogenizer (MP Biomedicals)

    An advanced, high-speed benchtop homogenizer used for lysis of any type of cells, tissues, bacteria, fungi, plants, soil samples, etc.

    mpbio.com

  • Qubit 3.0 Fluorometer

    Used for the quantitation of DNA, RNA, microRNA, and protein, using the highly sensitive and accurate fluorescence-based assays. Used widely for NGS applictions.

    thermofisher.com

  • Eppendorf epMotion 5070 Liquid Handling Workstation

    Used for routine applications which involves automated pipetting systems such as serial dilutions, reagent distribution, sample transfer from tubes to plates, and sample normalization. to assist with nucleic-acid isolation, nucleic-acid quantitative and qualitative analysis, NGS library preparation, quantitative-PCR analysis, etc.

    eppendorf.com

  • Agilent Mx3005P qPCR System

    High-performance real-time qPCR system. Ideal for a wide variety of applications and chemistries. It has four optical channels, allowing multiplexing with most fluorescent dyes.

    genomics.agilent.com

  • Thermo Scientific Savant DNA120 SpeedVac

    High-performance concentrator for efficient concentration, and drying of small-volume DNA or RNA samples.

    thermofisher.com

Other Services

GRL maintains Supply Center and Freezer Program located in Morrill 4, N214. Bio-Rad, New England Biolab (coming soon).
GRL and Integrated DNA Technologies (IDT) have created a portal for Discounted Primer orders. Visit www.idtdna.com/umamherst for more information

   
Tech Fee $60/hour
Agilent Mx3005P qPCR System Equipment Fee $5/hour
Eppendorf Mastercycler epGradient Equipment Fee $5/hour
Agilent 2100 Bioanalyzer Equipment Fee $10/hour
Agilent 2100 Bioanalyzer DNA HS assay $85/assay
Agilent 2100 Bioanalyzer DNA 7500 assay $62/assay
Agilent 2100 Bioanalyzer RNA 6000 Nano assay $67/assay
Agilent 2100 Bioanalyzer RNA 6000 Pico assay $69/assay
Syngene Ugenius Agarose GelDoc System Equipment Fee $5/30 minutes
Agarose gel DNA analysis (DNA ladder, sample run + image)
(minimum 2 sample rate)
$5/sample
Qubit Equipment Fee $3/15 minutes
Qubit dsDNA BR, dsDNA HS, RNA BR, RNA HS Assays $3/sample
BluePippin Equipment Fee $10/hour
BluePippin sample prep
(Additional 1 lane rate for external marker cassette)
$28/sample
Bioruptor Pico Equipment Fee $14/hour
Bioruptor Pico sample processing
(Minimum 8 sample rate)
$5/sample
Savant SpeedVac DNA120 Equipment Fee $5/hour
Fast Prep-24 5G Equipment Fee $10/hour
MiSeq Reagent Nano Kit v2 (300 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$398/assay
MiSeq Reagent Nano Kit v2 (500 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$493/assay
MiSeq Reagent Micro Kit v2 (300 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$585/assay
MiSeq Reagent kit v2 (50 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$935/assay
MiSeq Reagent kit v2 (300 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1178/assay
MiSeq Reagent kit v2 (500 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1311/assay
MiSeq Reagent Kit v3 (150 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1041/assay
MiSeq Reagent kit v3 (600 Cycle kit)
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1796/assay
NextSeq500 Mid-150 cycle kit
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1206/assay
NextSeq500 Mid-300 cycle kit
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1876/assay
NextSeq 500 High-75 cycle kit
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$1571/assay
NextSeq 500 High-150 cycle kit
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$2971/assay
NextSeq 500 High-300 cycle kit
(Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)
$4891/assay
Library Prep: DNA (Shotgun Metagenome / Genome, ChIP)
(minimum 2 sample rate)
$101/sample
Library Prep: Total RNA (no rRNA reduction and no poly(A)
(minimum 4 sample rate)
$118/sample
Library Prep: poly (A) mRNA, stranded, (minimum 4 sample rate) $140/sample
Library Prep: QuantSeq 3′ mRNA-Seq Kit FWD or Rev for Illumina
(minimum 6 sample rate)
$75/sample
Library Prep: Targeted Amplicon Sequencing (16S, 18S rRNA)
(minimum 10 sample rate), (custom primers addtional fee may be applied)
$18/sample
Library Prep: Small RNA (microRNA)
(minimum 6 sample rate)
$168/sample
Library Prep: Single Cell/Low Input RNA Library Prep for Illumina
(minimum 6 sample rate)
$149/sample
Library Prep: Illumina NexteraXT (for FLDGM cDNA), 96 Well format $1998/96W plate
NEBNext rRNA Depletion Kit (Human/Mouse/Rat)
(minimum 4 sample rate)
$74/sample
MICROBExpress Bacterial mRNA Enrichment Kit
(minimum 4 sample rate)
$48/sample
NGS Library QC (qPCR assay)
(minimum 2 sample rate)
$16/sample
DNA Isolation $18/sample
RNA Isolation $29/sample
Illumina MiSeq Equipment Fee $100/24 hours
Illumina NextSeq 500 Equipment Fee $200/12 hours
Fluidigm C1 Autoprep system Equipment Fee $120/assay
Fluidigm C1 Autoprep system Assisted Fee
Supplies (IFC, IFC Imaging, cell & mRNA reagents provided by PI, as pass through cost)
$362/assay
Limited Data Analysis
(Additional one sample rate per group comparison)
$25/sample
Sample dilution/pooling $1/sample
PhiX Spike-in $15/sample
Custom Primer (Eg., 16S Seq by GRL) $15/assay

For any failed unassisted/assisted runs, additional diagnostic fees may be applied.
Training Fees and supplies additional.
No show/cancellation for equipment reservation fees may be applied. Cancellation before 48 hours no fees charged.
Rates are subject to change, contact facility to verify current fees.

 

Services

Training

Training for new users consists of:

  • lab safety training as mandated by UMass EH&S,
  • operation of the instrument and associated software,
  • use of data analysis software,
  • exporting or presenting data,
  • clean up and shutdown of the instrumentation.

Once the training is complete, researchers may schedule their experiments through the director of the GRL (Ravi Ranjan).

 

Ravi Ranjan, MSc, PhD
Ravi joined IALS in 2017, as a Senior Research Fellow/Director of the Genomics Resource Laboratory at UMass Amherst. He is involved in managing the Genomics Facility, and providing Next-Generation Sequencing (NGS) services, from sample preparation to generation of high throughput sequencing data. He provides instrumentation training, NGS project consultation, technical assistance, and documentation for grants application and manuscripts. His research interests are in the field of Molecular Microbiology and Microbiome research. He is interested to introduce new technologies and develop new SOPs related to NGS.

Freezer Program and Supply Center

Dear UMass IDT Portal Users –

"UMass IDT Portal Temporarily Discontinue from July 01, 2018"

Due to ongoing logistical and technical issues with managing the portal from IDT, we plan to freeze (temporarily discontinue) the portal from July 01, 2018 onwards. IDT plans to roll out the renewed portal. Once we resolve the ongoing issues, we will be live again.

Meanwhile, users can plan to switch and place the orders from IDT directly or their preferred vendor.

We apologize for any inconvenience. Thank you for understanding and your kind cooperation.

Thank You,
Ravi Ranjan, PhD
Genomics Resource Lab, UMass Amherst

List of Reagents currently provided by Genomics Facility

Vendor Product Name Cat/SKU # Vol/Reaction Fee
Life Tech Qubit dsDNA BR Assay Q38253 1 assay and tube $1.10
Life Tech Qubit dsDNA HS Assay Kit Q32854 1 assay and tube $1.10
Life Tech Qubit RNA BR Assay Kit Q10210 1 assay and tube $1.90
Life Tech Qubit RNA HS Assay Kit Q32852 1 assay and tube $1.90
Teknova 10 mMTris-HCl + 0.1% Tween 20 T7724 1 ml $3.50
Beckman Coulter Agencourt AMPure XP Beads A63880 1 ml $27.00
Diagenode Bioruptor Pico Tube (0.2 ml) C30010020 1 tube $0.75
MP Biomedicals FastPrep 24 5G Homogenizer
Tubes(2 ml tube with Green cap)
  1 tube $0.75
  Use the form (GRL-Reagent_v2) to request reagents.
Mention reagent amount and pick up time in the form. Contact GRL for reagent availability and pick-up.
Rates subject to change any time. Customers will be charged, based on the order date.
Reagents availability subject to change any time.
Updated January 21, 2018

 

Volunteer Position

The Genomics Research Laboratory at Institute for Applied Life Sciences, is looking for volunteer(s) to assist with day to day routine lab activities, managing inventory and instruments, assisting with protocol development (schedule and experience permitting). Ideal for students who are looking forward to pursue research. For more information visit www.umass.edu/ials/genomics

Requirements: Undergraduate (freshman) preferred with biology back ground. Flexible lab hours. Lab hours can be coordinated with class schedule. Please note this is temporary and an unpaid position. Interested candidates please send CV at ranjan@umass.edu with subject heading: GRL_Volunteer_(your name)

For further information contact
Ravi Ranjan, PhD,
Director, Genomics Research Laboratory
Morrill 1, N330
Phone Office: 413-577-4501
Email: ranjan@umass.edu

Institute for Applied Life Sciences

N510 Life Science Laboratories
240 Thatcher Road
Amherst, MA 01003-9364
contactials@umass.edu | 413-545-1710

Massachusetts Life Sciences Center