Core facilities

Genome Center Core Facilities

Users of the Genome Center Core Services can set up an account which will enable you to use all the core facilities.

 

Bioinformatics Core

Website: http://bioinformatics.ucdavis.edu — Email: bioinformatics.core@ucdavis.edu

Core Manager: Dr. Ian Korf
Core Office: 530-752-2698

The Bioinformatics Core provides expertise and infrastructure for the acquisition, curation, analysis, and distribution of large complex biological datasets, with an emphasis on sequence data. We offer data analysis services, free consultations for grant or project planning, and training aimed at empowering graduate students, post-docs, and PIs to do their own bioinformatics data analysis. Also, we can help you design, install, and maintain your lab’s high performance computing infrastructure, providing stable support even as lab members come and go. Please send us an email or call (530-752-2698) with your questions, or visit our website to find out more about how we can help you.

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DNA Technologies Core

Website: http://genomecenter.ucdavis.edu/dna_technologies — Email: dnatech@ucdavis.edu

Core Manager: Dr. Lutz Froenicke
Lab: 530-754-5281, Fax: 530-754-9658

The DNA Technologies Core provides Illumina high-throughput sequencing, PacBio long read sequencing, as well as Fludigm EP1 and Illumina BeadArray high throughput SNP genotyping. The Core further offers many sequencing-associated services such as library preparation and QC, as well as consultations on project design. Downstream analytical options can be coordinated with the Bioinformatics Core.

High throughput DNA sequencing (e.g. whole genome, targeted sequencing, transcriptome, ChIP-seq, metagenome) and variant detection is available using Illumina HiSeq and MiSeq sequencers that generate up to 600 Megabasepairs of sequence each run (HiSeq), with read lengths of up 2 x 300 bp (MiSeq). The PacBio RS instrument generates long reads (up to ~8 Kbp average length and maximum read lengths of more than 20 Kbp).

For SNP genotyping the Fluidigm EP1 platform offers efficient low- to mid-multiplex SNP genotyping at customizable scale.  The Illumina GoldenGate Assay can analyze 384 to 1,536 SNPs/sample, and the Infinium platform can analyze from 7,600 to over 1,000,000 SNPs per genotype. Advice on project design is also available and we have experience in working with data from a diverse range of plant and animal species.

Several items of equipment (Molecular Devices plate reader, Nanodrop, Bioanalyzer, Covaris and Bioruptor sonicators, Caliper SciClone liquid handler, Caliper Gx, Fluidigm Access Array, Fluidigm C1) are available for use by members of the research community after training by Core personnel (for a nominal annual fee).

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Expression Analysis Core

Website: http://genomecenter.ucdavis.edu/expression_analysis — Email: dnatech@ucdavis.edu

Core Manager: Dr. Lutz Froenicke
Lab: 530-754-5281, Fax: 530-754-9658

The Expression Analysis Core offers many RNA-seq options such as ribosomal RNA-depletion, polyA enrichment, strand-specific sequencing, and ultra-low input libraries.  Multi-day RNA-seq library prep workshops are also offered on a regular basis. The Illumina BeadArray gene expression platform is available for expression studies in human and mouse.

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Metabolomics Core

Website: http://metabolomics.ucdavis.edu — Email: metabolomics@ucdavis.edu

Core Manager: Dr. Oliver Fiehn
Lab: 530-754-8553, Fax: 530-754-8370

The metabolomics core provides untargeted and metabolite target analyses for a wide range of biochemical pathways, covering over 1,200 identified metabolites with validated analytical methods and known mass spectra and retention times. The facility utilizes 8 LC-MS and 7 GC-MS instruments with both nominal mass and accurate mass capabilities. The core is happy to engage in project specific method development and implementation.

The core further provide services in univariate and multivariate statistical analysis of data sets, pathway analysis and mapping, partial correlation and network analysis. We are looking forward to collaborate with you for turning your metabolomic data into biologically significant discoveries!

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Proteomics Core

Website: http://proteomics.ucdavis.edu — Email: proteomics@ucdavis.edu

Core Manager: Dr. Brett Phinney
Lab: 530-754-5298, Fax: 530-754-8370

The Proteomics Core provides state-of-the-art analytical proteomic services with particular emphasis on label free quantitative proteomic profiling, the analysis of macromolecular complexes, the post-translational modification of their constituents and standard protein identification from complex protein mixtures.

The Core, has a staff of six individuals including two Ph.D. scientists. For high throughput identification and characterization of proteins and peptides the Core has at its disposal several state of the art LC-MS/MS systems including a new Thermo Scientific Q-Exactive Orbitrap mass spectrometer connected to an EASY nLC II system, a LTQ-FT Ultra hybrid Fourier Transform Ion Cyclotron tandem mass spectrometer connected to a Waters Acuity Ultra High Pressure Nano UPLC, two Thermo Scientific LTQ tandem mass spectrometers connected to a Michrom Paradigm HPLC’s, and a Thermo Scientific TSQ Vantage Triple Quadrupole mass spectrometer for quantitative multiple reaction monitoring (MRM) targeted proteomics experiments. Core personnel can also provide amino acid analysis using one of three Hitachi amino acid analyzers and N-terminal sequencing using one of two N-terminal sequencers if needed.

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TILLING Core

Website: http://tilling.ucdavis.edu/ — Email: genome.tilling@gmail.com

Core Manager: Dr. Luca Comai
Lab: 530-754-1316

The TILLING Core provides mutants for rice, Arabidopsis thaliana, and tomato as well as other species on request. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetic technique that uses chemical mutagenesis to create libraries of mutagenized individuals that are subjected to high-throughput sequencing for discovery of mutations.

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Upcoming Talks and Events

  • October 17, 2014
    • David Rocke — Differential Expression Analysis with RNA-SEQ: Review and Critique
      Starts: 9:00 am
      Ends: October 17, 2014 - 10:00 am
      Location: GBSF 4202
      Description: Structural & functional genomics focus group meeting

      Speaker: David Rocke, Public Health Sciences and Biomedical Engineering.

      Abstract

      RNA-Seq data are increasingly used for whole-genome differential mRNA expression analysis in lieu of gene expression arrays such as those from Affymetrix and Illumina. We review commonly used methods for this type of analysis, including DESeq, edgeR, and Cuffdiff2, by placing them within a common framework that allows comparisons of components of the methods as well as of the overall results. We also review a number of recent studies comparing these methods in terms of false positives and sensitivity, and add additional results of our own. We show that none of the existing methods is fully satisfactory, with most identifying large numbers of genes as differentially expressed even when there are none, but some will lead to better, more reliable results than others. This area is still early in its intellectual development and is changing rapidly. This has important implications for how applied researchers should approach the analysis of their RNA-Seq data and how these analyses should be documented.
    • Dr. Nissim Hay— The Role of Akt Isoforms in Cancer and Diabetes: Lessons from Akt KO Mice
      Starts: 9:00 am
      Ends: October 17, 2014 - 10:00 am
      Location: UCDMC Cancer Center Auditorium, Sacramento
      Description: Cancer Center Biology Seminars
    • Daniela Barile — Milk bioactive compounds: prebiotic effect and beyond
      Starts: 12:10 pm
      Ends: October 17, 2014 - 1:00 pm
      Location: GBSF 1005
      Description: MMI 291 Seminar Series: "Emerging Challenges in M
      icrobiology and Immunology"

      Speaker: Daniela Barile, Ph.D., Assistant Professor, Food Science and Technology, University of California, Davis
    • Dr Sriram Subramaniam — Applications to HIV/AIDS and signal transduction: cryo-electron microscopy comes of age
      Starts: 2:00 pm
      Ends: October 17, 2014 - 3:00 pm
      Location: LSA 1022
      Description: Dr Sriram Subramaniam is from the National Cancer Institute, NIH, Bethesda

      Abstract: Recent breakthroughs in the field of cryo-electron microscopy provide new opportunities for determination of the structures of a variety of macromolecular assemblies and small dynamic protein complexes that are not amenable to analysis by X-ray crystallography or NMR spectroscopy. In addition, advances in technologies for imaging whole cells and tissues in 3D at high resolution have opened up new vistas for 3D structural imaging. The long-term mission of our research program is to obtain an integrated molecular understanding of viral and cellular architecture by combining advanced technology development for 3D imaging with novel methods for image segmentation and computational analysis. Specific areas of current interest that I will discuss include: structural biology of HIV entry, mechanisms of membrane transport, and assembly of protein complexes involved in metabolism.
  • October 20, 2014
    • Dr. Charlie Gersbach — Editing the Human Genome and Epigenome with the CRISPR/Cas9 System to Correct Genetic Disease and Program Cell Phenotype
      Starts: 10:00 am
      Ends: October 20, 2014 - 11:00 am
      Location: GBSF 1005
      Description: Dr. Gersbach (Duke University) is a leader in genome engineering. He is the 2014 recipient of the Outstanding Young Investigator Award by the American Society for Gene and Cell Therapy (ASGCT), largely for this work with Duchenne Muscular Dystrophy.
    • Marty Usrey — Dynamic Properties of Neural Circuits for Vision
      Starts: 12:10 pm
      Ends: October 20, 2014 - 1:00 pm
      Location: 1022 Life Sciences
      Description: Neurobiology, Physiology & Behavior 2014 Fall Faculty Seminar Series.

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