Genomics

The Genomics Research Core Facility applies state-of-the-art next generation sequencing (NGS) technologies to interdisciplinary biomedical, biochemical and biological research. Adapting fast developing NGS tools, our key applications include whole genome resequencing for genome-wide polymorphism and mutation detection, transcriptome profiling for quantification of gene expression and discovery of novel transcripts, alternative splicing events and transcribed SNPs, sequencing of bisulfite-treated DNA for detection of methylated DNA, chromatin immunoprecipitation-sequencing (ChIP-seq) for genome-wide mapping of protein-DNA interactions, microbial metagenomic sequencing, small RNA sequencing, etc. For each application, we offer comprehensive services from high quality nucleic acid extraction, NGS library preparation and sequencing to bioinformatic data analysis, as well as consultation and training.

Image showing overview of the workflow from Library Prep to Sequencing to Data Analysis

The Genomics Core Facility houses:

Contact Information:
Amy Gordon, Ph.D.
Genomics Research Core Director
518-276-4117
gordoa2@rpi.edu


 
 

Sample Requirements

Only DNA and RNA samples are accepted in compliance with RPI Institutional Biosafety Committee protocols and policies.

 
Note: for dsDNA library, use the following formula to convert from ng/μl to nM: (concentration in ng/μl) / (600 g/mol x average library size in bp) x 106 = concentration in nM
Sample Typegenomic DNAtotal RNAself-prepared library
Sample Purity (OD260/280)1.8-2.01.8-2.01.8-2.0
Recommended RIN/≥ 7.0/
Recommended Quantity>5 µg, >100 ng/µl>3 µg, >100 ng/µl10-50 nM, ≥ 10ul
Resuspension Buffernuclease-free water, EB, or low TE buffernuclease-free waternuclease-free water, EB, or low TE buffer
Shipment Methoddry icedry icedry ice

Service Request

Step 1 - Request a project: 

  • For iLab users, click on https://rpi.corefacilities.org/account/login to log in the Genomics core iLab website. Under ‘Request Services’ tag, click ‘initiate request’ button to fill in project information step by step. 
  • For other users, please email to gordoa2@rpi.edu. New iLab account can be set up by request. 

Step 2 - Submit sample information:

  • For iLab users, templates of sample information will be provided in the system while you fill in your project request. Please download and fill in the template form, change file name (such as user_date) and upload back to iLab.    
  • For other users, if you submit samples for NGS library preparation and/or QC, please download and fill in the Template of Library Prep and email to gordoa2@rpi.edu. If you submit self-prepared dsDNA libraries for sequencing, please download and fill in the Template of Sequence Self-prepared library and email to gordoa2@rpi.edu. 

Step 3 - Deliver nucleic acid samples to the Genomics Core:

  • Pack according to the sample requirement and label tubes clearly. A sample list is recommended within the package.
  • For non-RPI users, if you order Illumina sequencing kit yourself, please directly ship it from the vendor to our core facility.
  • Mailing Address:

    Amy Gordon
    Rensselaer Polytechnic Institute
    BioTech Bldg BT2434
    110 8th Street
    Troy NY, 12180-3590

Data storage

Sequencing and Analysis data will not be stored in the core server beyond 6 months.

Consultation

Monday and Thursday 4:00 pm -- 5:00 pm consultation is free of charge.  Other time consultation is by appointment only with hourly personnel fee.

Hours

Monday to Friday 9:00 am to 5:00 pm

Billing

Users will be required to provide billing information prior to requesting services. Users with multiple billing accounts should specify the account number to be charged upon sign-up. Both internal and external users will be billed on a monthly basis. Providing fraudulent and/or inaccurate billing information may result in the loss of use privileges.

Technology and Service:

image of code on a computer screen
Library Preparation and Bioinformatics Analysis
Standard and custom library preparation services are available for diverse short-read and long-read sequencing strategies. Bioinformatics services include established and emerging pipelines for transcriptomic, genomic and epigenomic applications.
Illumina NextSeq 550
Illumina NextSeq 550
The NextSeq 550 offers flexible high-throughput sequencing capacity for exome, transcriptome and whole-genome sequencing of all sizes of genomes, as well as the ability to scan microarrays. It generates up to 120 Gb of sequence data overnight and allows a variety of output configurations for optimized target genome coverage.
Illumina iSeq 100
Illumina iSeq 100
The iSeq 100 sequencing system is Illumina’s most accessible, cost-effective and rapid benchtop sequencer powered by CMOS technology and SBS chemistry. It generates 1.2 Gb of data per run.
Oxford Nanopore MinION at Rensselaer
Oxford Nanopore MinION
The Oxford Nanopore MinION is a portable real-time sequencing device generating ultra-long reads from single DNA or RNA molecules without PCR amplification. Each MinION run generates 10-20 Gb of raw data with 75% of these reads passing quality control filters.
Close up image of the Genomics 10x Next GEM
10x Genomics Chromium
The 10x Genomics Chromium Controller is an advanced automated microfluidics system that partition and barcode input suspensions of single cells or nuclei for single cell gene expression, ATAC and immune profiling studies. Each Chromium chip can process up to eight samples in parallel with 500-10,000 cells per sample. The finished single cell libraries are compatible with Illumina sequencing platforms.
Sage Science BluePippin
BluePippin DNA size selection system
The Sage Science BluePippin system is an automated DNA size selection tool for NGS applications, plus the capability of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA up to 50 kb.
close up image of the QIAcuity digital PCR
QIAcuity digital PCR
QIAcuity digital PCR is a fully automated nanoplate-based system providing highly sensitive and absolute nucleic acid quantification of up to five channels per sample. Digital PCR is particularly useful for detecting targets of low-abundance or in complex backgrounds, allelic variants, and for monitoring subtle changes that cannot be accurately quantified by real-time PCR.
Close up image of the epMotion 5075 liquid handler
epMotion 5075 liquid handler
The epMotion 5075 system offers fast, accurate and reproducible pipetting automation for diverse liquid handling demands. The 5075 model is equipped with a magnetic plate, a thermo mixer, a thermos block, a vacuum unit, and UV and HEPA filter. The system is used in DNA/RNA extraction, NGS library preparation, immunoassays, PCR plating, plate reformatting and other general pipetting tasks.
Close up of the Bio-Rad
Bio-Rad CFX qPCR
Genomics Core has two Bio-Rad qPCR systems: CFX96 and CFX384. The CFX96 with a 96-well thermal block can detect fluorescent signals in up to five channels, providing high thermal uniformity and accurate quantification for general real-time PCR applications. The CFX384 has a 384-well thermal block detecting fluorescent signals in up to four channels.
Agilent 2100 Bioanalyzer
Agilent 2100 Bioanalyzer
The Agilent 2100 Bioanalyzer system is an established automated electrophoresis solution for the quality control of biomolecule samples. The system integrates an instrument, data processing software, reagents, and a microfluidic chip specific for DNA, RNA or protein analysis.
Invitrogen Qubit 4 Fluorometer
Invitrogen Qubit 4 Fluorometer
Qubit 4 fluorometer measures very low level of DNA, RNA, and protein concentration using as little as 1 μL of sample. It has higher sensitivity than UV absorbance–based quantification instruments, such as NanoDrop. RNA integrity values can also be quantified for total RNA samples.

Required Acknowledgement and Authorship

Please acknowledge the CBIS Core Facilities in all publications and grant applications where our equipment and/or personnel have facilitated the work. These acknowledgements are very important because documenting our contributions helps to ensure that the resources of the Core Facilities are sustainable.

  • Equipment: If you used Core Facility equipment, please note this in the Materials and Methods. e.g., Thermogravimetric analysis was carried out using a TA Instruments TGA-Q50 (Rensselaer CBIS Analytical Biochemistry Core Facility).
  • Personnel: Please consider including CBIS personnel as co-authors on your publications when they have made a significant intellectual contribution to the research. Include CBIS Core Facility directors or staff as co-PI or co-investigators in grant applications when they provide a significant contribution to the grant proposal and scientific/intellectual leadership for the proposed work. Please follow these guidelines: ABRF Recommended Guidelines for Authorship on Manuscripts. Also, our Core Facility personnel always appreciate when they are mentioned in the Acknowledgements section of publications.
  • Required Funding Authorization Form: Rensselaer researchers must fill out the CBIS Cores Authorization Form (PDF) to use the CBIS Core Facilities.

Shirley Ann Jackson, Ph.D. Center for
Biotechnology and Interdisciplinary Studies

1623 15th Street

518-276-4259

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