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

Events on October 23, 2014
Paul Kirk — Bayesian Inference for tumor heterogeneity using the Hamming Ball Sampler
Starts: 2:00 pm
Ends: October 23, 2014 - 3:00 pm
Location: GBSF auditorium
Description: Presenter: Paul Kirk, Department of Statistics and Wellcome Trust Centre for Human Genetics, University of Oxford, UK

Abstract: The characterization of sub-clonal structure from whole genome sequencing of heterogeneous tumors is a computationally challenging problem due to the large number of mutations and unknown number of tumor sub-populations. Many recent approaches have adopted methods based on Bayesian nonparametric models (the Dirichlet or Indian Buffet Process) but standard computational methods for inference for these models can be slow as they rely on inefficient Markov Chain Monte Carlo methods. We have developed a novel Markov Chain Monte Carlo sampling algorithm that allows efficient and exact Bayesian inference for multiple membership models that is scalable to massive datasets. While standard approaches use asymmetric updates that are prone to becoming trapped in local modes, our algorithm uses locally symmetric modes that allows joint updating of the latent variable structure. We illustrate the utility of the sampling algorithm for tumor deconvolution problems and demonstrate its advantage over standard computational alternatives.
For questions, or to meet with the speaker, please contact Luis Carvajal-Carmona (lgcarvajal@ucdavis.edu) or John Williamson (jbwilliamson@ucdavis.edu)
Diana Wall — Lessons from an Antarctic Desert Documenting Climate Change and Measuring its Impact on Soil Life
Starts: 4:10 pm
Ends: October 23, 2014 - 5:10 pm
Location: 3 Kleiber Hall
Description: Diana Wall:
University Distinguished Professor, Department of Biology Director, School of Global Environmental Sustainability Colorado State University

Dr. Wall is an internationally recognized ecologist for her research to explore how soil biodiversity contributes to healthy, productive soils and thus benefits society, and the consequences of human activities on soil sustainability. Her global research includes more than twenty years of research in the Antarctic Dry Valleys examining how climate change affects soil biodiversity, ecosystem processes and ecosystem services. Wall Valley, Antarctica was named for her achievements in 2005.
She serves as Science Chair for the Global Soil Biodiversity Initiative. A Board Member of the World Resources Institute, she has served also as President of the Ecological Society of America, the American Institute of Biological Sciences, the Association of Ecosystem Research Centers, the Society of Nemaologists, and Chair of the Council of Scientific Society Presidents. She is a Fellow of the American Association for the Advancement of Science, is a member of the American Academy of Arts and Science, and holds an Honorary Doctorate from Utrecht University, The Netherlands. Dr. Wall received the 2013 Tyler Prize for Environmental Achievement, which is the premier international award for environmental science, environmental health and energy conferring great benefit upon mankind.
Events on October 27, 2014
Gregg Recanzone — Listening with an Aging Brain
Starts: 12:10 pm
Ends: October 27, 2014 - 1:00 pm
Location: 1022 Life Sciences
Description: Neurobiology, Physiology & Behavior 2014 Fall Faculty Seminar Series.
Events on October 28, 2014
Arsalan Daudi — How we can address reproducibility, a missing piece in life science research
Starts: 1:10 pm
Ends: October 28, 2014 - 2:10 pm
Location: LSA 1022
Description: Postdoc seminar serires

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