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Core Facilities

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Genome Center Core Service Facilities

Users of the Genome Center Core Services can set up an account at http://cores.genomecenter.ucdavis.edu which will enable you to use all the genome center core facilities.

Bioinformatics Core http://bioinformatics.ucdavis.edu 


Dr. Ian Korf, Faculty Director - email: ifkorf@ucdavis.edu
Office: 530-754-4989, Fax: 530-754-9658

The Bioinformatics Core provides expertise and infrastructure for the acquisition, curation, analysis, and distribution of large complex datasets, as well as develop and perform computations, analyses and simulations addressing a wide variety of biological questions from genomics to network biology. The Core has seven staff members with overlapping expertise in computing infrastructure, Web/database, scientific programming, biological annotation and statistics. The Core provides bioinformatics support for the wetlab service cores as well as for researchers with individual bioinformatics needs.  The computing infrastructure of the Core includes: 1) high performance computing clusters: a 110-node cluster of 4-core AMD Opteron CPUs with 4GB of RAM (32 nodes have 8GB of RAM), a mixed cluster consisting of ~80 nodes of Intel and AMD Opteron CPUs (10 nodes have 32BG RAM); 2) data storage servers of 300TB spreading across several fileservers including three Sun X4500, Isilon storage cluster and Linux based fileservers; 3) backup servers: a 16TB fileserver in offsite for disk to disk backup, a Sun/StorageTek backup server with a 2TB disk array and a 30-slot LTO3 tape jukebox for tape backup; 4) ultra large memory machines: three servers with 128GB, 144GB and 512GB of RAM respectively; 5) application servers: a Windows server for Windows specific Bioinformatics software tools and work stations for software developers and guests; 6) cloud computing: a preserved instance in Amazon Cloud and tools to access scalable resources provided by the Amazon Cloud Services; 7) network bandwidth: a 10Gbit/s network connection to Corporation for Education Network Initiatives in California (CENIC) and National Lambda Rail.


DNA Technologies Core http://genomecenter.ucdavis.edu/dna_technologies 

Dr. Ryan Kim, Manager – email: rwkim@ucdavis.edu
Lab: 530-754-5281, Fax: 530-754-9658 

The DNA Technologies Core provides both high throughput sequencing and Single Nucleotide Polymorphism (SNP) analysis.   Multiple platforms provide the capability to run low to very high throughput SNP assays with no requirements on the minimum or maximum number of samples or SNPs analyzed.  Several Illumina platforms cover a wide range of projects: the BeadXpress system provides an economical and flexible system to analyze 1 to 384 SNPs/sample, the BeadArray system 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 available if required.  A diverse range of plant and animal species have been analyzed.  High throughput DNA sequencing (whole genome, transcriptome, ChIP-seq, metagenome) and variant detection is available using Illumina HiSeq, MiSeq, and GAIIx sequencers that generate up to several hundred Gigabases of sequence each run. The Core also has a PacBio RS that enables the sequencing of amplified or unamplified single stranded template; this instrument generates long reads with ~3kb average and up to 10kb.  Several items of equipment (plate reader, nanodrop, bioanalyzer, and bioruptor) are available for use by members of the research community with annual training and at a nominal fee. Sequencing template libraries can be made.  Initial base calling is provided; downstream analytical options can be carried out by the Bioinformatics Core.


Expression Analysis Core http://genomecenter.ucdavis.edu/expression_analysis 

Dr. Ryan Kim, Manager – email: rwkim@ucdavis.edu
Lab: 530-754-5281, Fax: 530-754-9658 


The Expression Analysis Core extends the services provided by the Genome Center/School of Medicine Affymetrix microarray facility.  The Illumina gene expression platform is available for expression studies in human, mouse, or rat.  Additional services include custom arrays, chromatin immunoprecipitation training, ChIP lab services, and comparative genomic hybridization using custom arrays.  The Illumina Sequencers and downstream data analysis pipeline are also available for expression and ChIP-seq projects.

 

Metabolomics Core http://www.metacore.ucdavis.edu

Dr. Oliver Fiehn, Faculty Director – email:  ofiehn@ucdavis.edu

Office:  530-754-8258, Lab: 530-754-8553, Fax: 530-754-8370

The Metabolomics Core provides high-quality, cost-effective, state-of-the-art analytical services for metabolomics research and small molecule analysis. The Core offers GC-MS and LC-MS lines for metabolic profiling using high quality standards, reagents, and solvents. It provides assistance with the experimental setup, design, data interpretation, and statistical analysis. The Core has a Pegasus III TOF mass spectrometer (Leco) coupled with Agilent GC and Gerstel autosampler, including the MPS PrepStation and AutomatedLinerEXchange (ALEX); a Thermo Electron LTQ (linear ion trap) mass spectrometer coupled to Surveyor HPLC separation system, and a Thermo-Fisher Scientific LTQ-FT Ultra Fourier transform ion cyclotron tandem mass spectrometer (FTICR) (shared with the Proteomics Core) coupled to NanoMate-ESI robotic device (Advion BioSciences). In addition, we have an Applied Biosystems Qtrap 4000 (shared with the Proteomics Core) coupled to Waters Acquity UPLC separation module equipped with the column manager; this system is perfectly suited for quantitative “targeted metabolomics” multiple reaction monitoring (MRM) experiments and LC/MS/MS quantitation available in triple quadruple mode.

 

Proteomics Core http://www.proteomics.ucdavis.edu 

Dr. Brett Phinney, Manager – email: bsphinney@ucdavis.edu
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.


Tilling Core http://tilling. ucdavis.edu/index.php/Main_Page 

Dr. Luca Comai, Manager email: genome.tilling@gmail.com 
Lab: 530-752-1316 

The TILLING Core provides mutants for rice, hexaploid and tetraploid wheat, 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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