Biotechnology Resource CenterGenomics Facility

Genomics Facility

 

    • Services include whole genome sequencing, targeted region sequencing, genotyping-by-sequencing (GBS), 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), and many other applications. Next generation sequencing instruments include Illumina HiSeq2500, NextSeq500, and MiSeq platforms. Sequencing library construction services 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- or 384-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.

  • 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.

  • Several instruments are available for digital PCR. These systems allow absolute or relative quantification using intercalating dyes or hydrolysis probes (e.q. Taqman assays).  Click here for more information.

  • 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. 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. Click here for more information.

    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. Click here for more information.

  • Services include SNP genotyping, structural variation, gene expression and gene regulation analysis using the Illumina and Agilent microarray platforms.  Click here for more information.

  • 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, bio-IT,  proteomics, imaging, and advanced technology assessment cores.  Click here for more information.

     

  • Includes genomics/bioinformatics seminars and workshops.  Click here for more information.