Genomics Resource Laboratory
Genomics Facility Operational Status
Operations return to normal.
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
- 16S/18S rRNA amplicon library prep
- 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 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.
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.
Bioruptor Pico Sonicator System
Sonication device for shearing DNA and RNA for NGS applications. Optimized for volumes of 20 - 100 μl.
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.
Agilent 2100 Bioanalyzer
Used for sizing, quantitation and quality control of DNA, RNA, and proteins.
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.
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.
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.
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.
Thermo Scientific Savant DNA120 SpeedVac
High-performance concentrator for efficient concentration, and drying of small-volume DNA or RNA samples.
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
|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||$4/30 mins|
|Agarose gel DNA analysis (DNA ladder, sample run + image), (minimum 2 sample rate)||$5/sample|
|Qubit Equipment Fee||$3/15 mins|
|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)||$501/assay|
|MiSeq Reagent Nano Kit v2 (500 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$643/assay|
|MiSeq Reagent Micro Kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$651/assay|
|MiSeq Reagent kit v2 (50 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,036/assay|
|MiSeq Reagent kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,280/assay|
|MiSeq Reagent kit v2 (500 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,499/assay|
|MiSeq Reagent Kit v3 (150 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,131/assay|
|MiSeq Reagent kit v3 (600 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,964/assay|
|NextSeq500 Mid-150 cycle kit (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,445/assay|
|NextSeq500 Mid-300 cycle kit, (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$2,141/assay|
|NextSeq 500 High-75 cycle kit, (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$1,870/assay|
|NextSeq 500 High-150 cycle kit, (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$3,306/assay|
|NextSeq 500 High-300 cycle kit, (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied)||$5,106/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)||$16/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||$1,998/96W 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|
|Illumina MiSeq Equipment Fee||$85/24 Hours|
|Illumina NextSeq 500 Equipment Fee||$216/24 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|
|Custom Primer (Eg., 16S Seq by GRL)||$15/assay|
For any failed unassisted/assisted runs, additional diagnostic fees may be applied.
Unassisted users for MiSeq and NextSeq 500. 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.
Training Fees and supplies additional
No show/ late cancellation for equipment reservation fees may be applied. (No cancellation fees charged for cancellation before 48 h for MiSeq and NextSeq 500.) (No cancellation fees charged for cancellation before 24 h for other equipment)
|Rates are subject to change, contact facility to verify current fees.|
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).
Service Request Forms
- Agilent Mx3005P qPCR System
- Agilent 2100 Bioanalyzer
- Bioruptor Pico
- Blue Pippin, Sage Science
- DNA Isolation/Extraction
- FastPrep-24 5G High Speed Homogenizer
- Illumina MiSeq
- Illumina NextSeq 500
- NGS Library QC
- Qubit 3.0 Fluorometer
- RNA Isolation/Extraction
- Thermo Scientific Savant DNA 120 SpeedVac
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.
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)
|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
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 firstname.lastname@example.org 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