Genomics Resource Laboratory

Genomics Resource Laboratory

Announcements

NextSeq 500 Services Discontinued

GRL will discontinue the NextSeq 500 related sequencing services and equipment support after 12/15/2023

 

Core Facilities Seminar

Rosha Poudyal, 10X Genomics–Biology at True Resolution: Resolve Biological Complexities with Single Cell and Spatial Solutions

Jennifer Rauch, Assistant Professor, Biochemistry & Molecular Biology and IALS–Introduction to the 10X Visium System and Applications

Replay on YouTube

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 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

  • 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

  • Thermo Scientific Savant DNA120 SpeedVac

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

    thermofisher.com

  • Bio-RAD CFX96 Touch Real-Time PCR Detection System

    The CFX96 Touch System is a powerful, precise, and flexible real-time PCR detection system. This six-channel (five colors and one FRET channel) real-time PCR instrument combines advanced optical technology with precise temperature control to deliver sensitive, reliable detection for singlexplex or multiplex reactions.

    bio-rad.com

  • 10x Genomics Chromium Controller

    The Chromium Controller uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale.

    10xgenomics.com

  • Nexcelom Cellometer K2 Fluorescent Cell Counter

    The Nexcelom Cellometer K2, powered by Matrix software, utilizes brightfield imaging and dual-fluorescence imaging to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.

    nexcelom.com

  • Qubit 4 Fluorometer

    The Invitrogen Qubit 4 Fluorometer accurately and quickly measures the concentration of DNA, RNA, or protein in a single sample. It can also be used to assess RNA integrity and quality. The easy-to-use touchscreen menus make it easy to select and run the assays you need, with results displayed in just a few seconds.

    thermofisher.com

Other Services

  • GRL maintains NEB NEBnow Supply Center.  
  • GRL (Dr. Ranjan) also provides services and consultation for preparing plasmid constructs (eg., gene expression), Sanger-Seq design, qPCR project design, Bacterial and Mammalian Cloning, etc.  
    Campus Users External Academic Industry
Tech Fee hour $86 $99 $111
Bio-RAD CFX96 Touch Real-Time PCR Detection System Equipment Fee hour $15 $18 $20
Eppendorf Mastercycler epGradient Equipment Fee hour $6 $6 $7
Agilent 2100 Bioanalyzer Equipment Fee hour $21 $24 $27
Agilent 2100 Bioanalyzer DNA HS assay assay $119 $136 $154
Agilent 2100 Bioanalyzer DNA 7500 assay assay $93 $107 $121
Agilent 2100 Bioanalyzer RNA 6000 Nano assay assay $102 $117 $133
Agilent 2100 Bioanalyzer RNA 6000 Pico assay assay $130 $147 $166
Syngene Ugenius Agarose GelDoc System Equipment Fee 30 minutes $4 $5 $6
Agarose gel DNA analysis (DNA ladder, sample run + image), (minimum 5 sample rate), plus TechFee sample $5 $5 $6
Qubit 4 Fluorometer Equipment Fee 30 minutes $5 $5 $6
Qubit dsDNA BR, dsDNA HS, RNA BR, RNA HS Assays (minimum 2 sample rate)  sample $5 $6 $6
BluePippin Equipment Fee hour $21 $24 $27
BluePippin sample prep (Minimum 2 sample rate, Additional 1 lane rate for external marker cassette). Only limited % gel assay) sample $76 $87 $98
Bioruptor Pico Equipment Fee hour $21 $24 $27
Bioruptor Pico sample processing (Minimum 8 sample rate) plus Tech and Machine fees sample $5 $6 $7
Savant SpeedVac DNA120 Equipment Fee hour $11 $12 $14
Fast Prep-24 5G Equipment Fee hour $20 $23 $26
MiSeq Reagent Nano Kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $648 $746 $843
MiSeq Reagent Nano Kit v2 (500 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $862 $991 $1,120
MiSeq Reagent Micro Kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $862 $991 $1,120
MiSeq Reagent kit v2 (50 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $1,373 $1,579 $1,785
MiSeq Reagent kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $1,680 $1,932 $2,184
MiSeq Reagent kit v2 (500 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $1,986 $2,284 $2,582
MiSeq Reagent Kit v3 (150 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $1,502 $1,727 $1,952
MiSeq Reagent kit v3 (600 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) assay $2,588 $2,977 $3,365
Illumina MiSeq Equipment Fee 24 hours $126 $145 $164
Library Prep: DNA (Shotgun Metagenome / Genome, ChIP), (minimum 4 sample rate) sample $97 $112 $126
Library Prep: Total RNA (no rRNA reduction and no poly(A), (minimum 4 sample rate) sample $111 $128 $145
Library Prep: poly (A) mRNA, stranded, (minimum 4 sample rate) sample $127 $146 $165
Library Prep: Targeted Amplicon Sequencing (16S, 18S rRNA), (minimum 10 sample rate), (custom primers addtional fee may be applied) sample $16 $19 $21
Library Prep: Single Cell/Low Input RNA Library Prep for Illumina, (minimum 6 sample rate) sample $154 $177 $200
NEBNext rRNA Depletion Kit (Human/Mouse/Rat), (minimum 4 sample rate) sample $78 $89 $101
NGS Library QC (qPCR assay), (minimum 2 sample rate) sample $19 $22 $24
DNA Isolation sample $16 $19 $21
RNA Isolation sample $25 $26 $30
Sample dilution/pooling sample $1 $1 $2
PhiX Spike-in sample $16 $18 $21
Custom Primer (Eg., 16S Seq by GRL) assay $31 $35 $40
10x Genomics Chromium Controller Equipment Fee 24 hours $87 $100 $113
Library Prep: 10X Genomics Single Cell Gene Expression Profling Assay (3' RNA) assay $2,664 $3,064 $3,463
Nexcelom Cellometer K2 Fluorescent Cell Counter Equipment Fee 30 minutes $6 $6 $7
 
Note 1: Rates are inclusive of reagents. Vendors periodically adjust reagent cost. The cost will be adjusted accordingly. Rates are subject to change, contact facility to verify current fees.
Note 2: GRL provides many other custom services, please contact facility staff.
Note 3: For any failed unassisted/assisted runs, additional diagnostic fees may be applied.
Note 4: Unassisted users for MiSeq. Due to limited budget, the sequencers are under Bronze service plan. Under this plan there is no reagent replacement. Any failed runs will be borne by user.
Note 5: No show/ late cancellation for equipment reservation fees may be applied.
No cancellation fees charged for cancellation before 48 h for MiSeq.
No cancellation fees charged for cancellation before 24 h for other equipment)
Note 6: Limited/restricted access for unassisted equipment use to external users.
Note 7: *FY25 rates applicable as of April 1, 2024
Rates are subject to change, contact facility to verify current fees.

FY25 Specialized Service Center Approved 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).

 

Genomics Resource Facility: The facility provides as suite of services, including, but not limited to - Next-Generation Sequencing services (whole genome, shotgun metagenome, metatranscriptome, amplicon, exome sequencing, etc), quantitative-PCR analysis, nucleic-acid isolation, quantitative and qualitative analysis. To provide these services, the facility is equipped with Illumina MiSeq Sequencing System, 10x Genomics Chromium Controller, Nexcelom Cellometer K2 Fluorescent Cell Counter, Bioruptor Pico Sonicator System (Diagenode), BluePippin (Sage Science), Agilent 2100 Bioanalyzer system, FastPrep-24 5G Sample Homogenizer (MP Biomedicals), Qubit 4.0 Fluorometer (Life Technologies), Bio-RAD CFX96 Touch Real-Time PCR Detection System, Thermo Scientific Savant DNA120 SpeedVac, One Eppendorf Mastercycler epGradient and Two BioRad T100 thermal cycler (PCR), Gel electrophoresis system (Denville Scientific) and Gel-Documentation system (Model UGenius, Syngene).

FY25 Specialized Service Center Approved Fees

CORUM (access and reservations)

Ravi Ranjan, MSc, PhD, MB(ASCP)CM
Ravi joined IALS in 2017, as the Director of the Genomics Resource Laboratory at UMass Amherst. He supervises the Genomics Facility, providing Next-Generation Sequencing (NGS) services, from sample preparation, NGS library preparation to generation of high throughput sequencing data and data analysis. He provides instrumentation training, NGS project consultation, single cell genomics project consultation, technical assistance, documentation for grants application and manuscripts. Ravi also assists with any genomics or molecular biology projects that falls within his realm of expertise and interest. 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 and genomics research.

Ravi Ranjan Publications: https://scholar.google.com/citations?user=G7hUmMEAAAAJ&hl=en 

Ravi Ranjan LinkedIn: linkedin.com/in/ravichicago  

GRL maintains only the NEB Freezer (NEBnow) program (https://www.neb.com/en-us/nebnow/university-of-massachusetts-amherst-nebnow)

Below are instructions for access to the NEB "NEBnow" Supply center:

  1. New account set-up: Walk to NEB Freezer (Morrill 1, N328), Create “New Account” using touchscreen,
    or create your account online at http://go.neb.com/nebnowumassamherst
  2. You will receive Notification on the registered email for next steps.
  3. Call NEB (at the phone number provided in notification email) and provide your ProCard (Credit card) Information.
  4. After approval from NEB (usually very quick, same day), you are all set.
  5. You will get a PIN on the registered email, and you are ready to access the freezer.
  6. Log on the NEB Freezer, using your credentials for access to the freezer.
  7. For stocked items, user MUST scan barcode and before taking items. ProCard (credit card) is charged automatically. GRL will not send any invoice to the user.
  8. For non-stocked items, user can place “special order’ through the Kiosk. Use Special order Tab and place your order. Orders placed before or on Tuesday, are delivered same week Thursday ONLY. Special order placed after Tuesday are delivered following week Thursday. The Kiosk is stocked on/after Thursday after noon ( ~ 3 PM).

Note: Deliveries and restocking can be delayed due to inclement weather, non-availability of staff, campus closure, etc.

Special order: -20°C reagents are stored in the NEB Freezer in the “Special Order” Bin. Check your order and name on the package. No need to scan the special order, as it is already charged on the ProCard.

Special order: 4°C, Room Temp, and -80°C are stored at GRL (Morrill1, N330). Call at 7-4501 or 7-4502 to schedule pick-up.

2024

2023

2022

2021

2020

2019

2018

The genomics services were performed at the Genomics Resource Laboratory (RRID:SCR_017907), Institute for Applied Life Sciences, University of Massachusetts Amherst, MA.