Biotechnology Resource CenterGenomics Facility

Genomics Facility


    • Services include whole genome sequencing (WGS), targeted region sequencing, whole transcriptome, targeted gene expression and small RNA profiling (RNA-Seq), sequencing of DNA fragments isolated by chromosome immunoprecipitation (ChIP-Seq), detection of DNA methylation (Meth-Seq), rAmpSeq, 3' RNA-Seq and many other applications. Next generation sequencing instruments include Illumina HiSeq2500, NextSeq500, and MiSeq platforms. Sequencing library construction services and design-to-analysis project management and support are available.  Click here for more information.

      • Services include Sanger cycle sequencing of submitted samples (DNA templates), dye terminator removal cleanup, and data generation on ABI 3730xl capillary electrophoresis instruments.  Sequencing of plasmids and PCR products can be done using either standard sequencing primers or user provided custom primers.  Templates can be submitted individually or in 96-well plates.  Customized sequencing chemistries can be used for difficult-to-sequence templates, such as templates with high-GC content or large constructs like BACs.  We routinely provide  high quality data results and fast data return times.  Click here for more information.

      • Core users can submit 96- or 384-well plates of samples that they cycle sequenced and did dye terminator cleanup, submitted in a ready-to-load format for data generation on ABI 3730xl sequencing instruments. Click here for more information.

      • Services include microsatellite, AFLP and SNP genotyping of samples submitted in either 96- or 384-well plates for fluorescent DNA fragment analysis with up to five dye detection. Core users submit their samples in plates, ready-to-load on the ABI 3730xl instruments.  Core users supply the appropriate size standards for their samples.  The ABI 3730xl determines the size of the DNA fragments. Five fluorescent dyes allows multiplexing of up to 4 samples plus a size standard in every lane.  Click here for more information.

    • The Oxford Nanopore MinION is a protein nanopore sequencing device that is capable of generating ultra-long reads, some of them in excess of 100kb. Using this device, single DNA (or RNA) molecules are sequenced without the need for PCR amplification of the sample. Currently we specialize in sequencing high molecular weight DNA for genome assembly on the MinION. Each MinION run generates 5-15 GB of raw data in a 48 hour time period, with 70-80% of these reads passing filter. Obtaining high molecular weight DNA fragments of high purity is a critical part of the sequencing process. If you are considering using this platform for genome assembly, please set up a consultation to discuss all aspects of the project.
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  • The Genomics Facility offers services to support your projects from experimental design to data analysis.

    Applications include whole genome or transcriptome sequencing with de-novo assembly or reference mapping, SNP/variant calling, data imputation, expression analysis (RNA-Seq), 3’RNA-Seq and genetic mapping. 

    We coordinate with other other BRC core facilities if your project requires technologies outside of the genomics facility , e.g. flow cytometry, laser capture microdissection or mass spectrometry for proteomics or metabolomics.

    To get started, contact us at

    • A Life Technologies/ABI Viia7 instrument system for real-time PCR (rtPCR) is available for direct use by core users. This system allows quantitation of starting material (genomic DNA, plasmid, RNA), along with heterozygote detection and SNP genotyping, using either fluorescent probes or the SYBR green reagent for detection.  Users reserve time on this instrument, prepare the plates of reactions, and set up the analysis runs on this instrument.  The core offers training on the use of the Viia7.  Users need to be trained before accessing this instrumentation.  Gene expression and SNP genotyping analysis can be performed on samples in 96- or 384-well plate format.  Click here for more information.

    • The Bio-Rad QX200 droplet digital PCR system allows for DNA quantification using limiting dilutions of the target DNA in up to 20,000 sub-nanoliter droplets. The instrument uses Taqman assays with two color detection (FAM and VIC/HEX) on a single sample or Evagreen assays using only a pair of PCR primers. For more information, see the Bio-Rad website at this link, or contact the Director of the Genomics facility.

    • Inquire for access.

    • Inquire for access.

    •  Several instruments are available to the user for DNA or RNA quantification, including a Nanodrop spectrophotometer and a Qubit spectrofluorometer. Please contact the Genomics Facility for information on using these instruments.

    •  Several instruments are available to the user for DNA or RNA quantification, including a Nanodrop spectrophotometer and a Qubit spectrofluorometer. Please contact the Genomics Facility for information on using these instruments.

  • DNA and RNA extraction services are available for plant leaf tissue. Click here for more information.

    Additional services include: sample cleanup using column-based purification protocols, high molecular weight sample prep protocols, sample concentration/dilution, and sample re-array.

  • Sample quality assessment/quality control (QA/QC) is available for all services, including DNA/RNA quantifications and checking RNA and DNA sample purity and integrity using state-of-the-art equipment and protocols for quantifying nucleic acids (DNA and RNA) using fluorescent intercalating dyes, evaluation of fragment sizes by capillary or field inversion gel electrophoresis. The core provides recommendations for both DNA and RNA sample QA/QC.  Click here for more information.

  • Illumina sequencing library preparation services are available for next generation sequencing for both DNA and RNA samples.

    10X Genomics library preparation services are available for both single-cell RNA-seq library construction and genomic DNA library construction for their linked-read technology. 

    High-throughput, Full Service projects, incuding library preparation are available for sequencing small and large genomes (WGS or skim sequencing), 3’RNA seq (a cost-effective alternative to RNA seq), rAmpSeq (genotyping Maize and Casava) and custom genotyping applications. 

    Click here for more information.

  • The Genomics Facility, either independently or in collaboration with the Bioinformatics Facility, offers full service bioinformatics for standard or custom applications including de-novo assembly, reference mapping, SNP/variant calling, data imputation, RNA-Seq, 3’RNA-Seq and genetic mapping. These services can be used with existing data or as part of a fully managed project from experimental design through analysis. Please inquire at

  •  Professional molecular biology lab services are available for evaluating proof-of-concept or collecting preliminary data for new genotyping protocols or other nucleic acid-based applications.  Please inquire at

  • Consultation on project design and data analysis is available upon request. Software analysis tools are available through the core.  Coordinated project design consultation and data analysis support are available with the BRC bioinformatics,  proteomics, metabolomics, imaging, and biotechnology development facilities. 


  • The Genomics Facility offers training for user-accessible instruments, sample preparation and data analysis pipelines/software. Seminars from vendor-partners for practical training or exposure to new technologies and chemistries are hosted regularly.  Data analysis workshops are also presented in collaboration with the Bioinformatics Facility and/or other Cornell affiliates.