Genomics Services

DNA / RNA Sequencing

o Next generation sequencing

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 in the core include the Illumina MiSeq and Illumina HiSeq 2000/2500 platforms.  Sequencing library construction services are available.  Services with PacBio RS-I and RS-II platforms are also available.

o Sanger sequencing and fragment analysis

§ Full service DNA sequencing

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. 

§ Ready-to-load DNA sequencing

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.

§ Fragment analysis

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.

• Microarrays

Services include SNP genotyping, structural variation, gene expression and gene regulation analysis using the Illumina, Affymetrix and Agilent microarray platforms. 

 

  • Arrays for Gene Expression analysis:

 

 

  • Arrays from Agilent, Affymetrix, and Illumina can be run in the Genomics Facility. Information on the available arrays and formats can be obtained from the manufacturer's websites (www.agilent.com, www.affymetrix.com, or www.illumina.com). The Genomics Facility offers services for RNA QC, sample labeling, hybridization, and scanning of the arrays. For Agilent and Affymetrix arrays, users may perform the initial steps and the Genomics Facility offers hybridization and/or scanning services only.

 

  • Arrays for SNP genotyping:

 

 

  • The Genomics Facility can run SNP arrays from Illumina, Agilent, or Affymetrix. However, Illumina BeadChip arrays using either the GoldenGate or Infinium chemistries are the preferred kits for SNP genotyping, because of their ease of use and superior performance. Illumina has stock arrays for many species, but also can create custom content arrays. More information can be found on the Illumina website (www.illumina.com) for what arrays are currently available, and information about designing custom SNP genotyping arrays. The Genomics Facility cannot scan some of the higher-density arrays available from Illumina. Therefore, before initiating any SNP genotyping project, it's strongly advised to consult our expert about the different options available.

 

  • Arrays for CGH, ChIP-on-chip, microRNA expression, etc.:

 

 

  • Arrays for applications other than gene expression or SNP genotyping are less frequently done in the Genomics Facility and it's advised to consult before initiating such projects.

 

  • Software for data analysis:

 

 

  • Several softwares are available through our facility for analyzing microarray data. In addition to free softwares available directly from the array manufacturers, we have several licensed softwares available by remote access on our servers. For gene expression analysis, GeneSpring is available, and for analyzing Illumina SNP genotyping array data, Illumina's GenomeStudio is available. These softwares are made available, free of charge, to anyone generating their data in the Genomics Facility.

• Real-time PCR

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. 

• Digital PCR

A Life Technologies/ABI QuantStudio3D system for digital PCR is available. This system allows absolute or relative quantification using Taqman assays and limiting dilution of DNA targets in a microchip format. 

• Sample preparation

Sample quality assessment/quality control (QA/QC) is available for all services, including checking RNA and DNA sample purity and integrity on the Agilent BioAnalyzer or quantification using a NanoDrop spectrophotometer or Qubit spectrofluorimeter.  The core provides recommendations for both DNA and RNA sample QA/QC.  Sample preparation (sequencing library construction) services are available for next generation sequencing for both DNA and RNA samples. 

• Consultation

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. 

• Workshops and training

Includes genomics/bioinformatics seminars and workshops. 

 

 

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