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: 530-754-9143, 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: 530-754-9143, 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 February 20, 2015
Seminar — Dr Hao Chen — Allele-specific copy number profiling by next-generation DNA sequencing
Starts: 9:00 am
Ends: February 20, 2015 - 10:00 am
Location: GBSF Room 4202
Description: Part of the Genome Center Structural and Functional Genomics Seminar Series


Abstract

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in giving a more complete portrait of tumor genomes and the inference of their clonal history. We propose a novel method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normal. Falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. We applied this method in the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allow us to draw detailed conclusions regarding the clonal history of the individual’s colon cancer.
Events on March 4, 2015
Dr Janine LaSalle — Seminar — Mapping the Placental Methylome at the Interface of Genetics and Environment in Autism Risk
Starts: 12:00 pm
Ends: March 4, 2015 - 1:00 pm
Location: Center for Health and Technology room 1341, 4610 X St Sacramento
Description: Part of the Human Genomic Seminar Series

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