See schedule of course here

See general info. here

See photos of course here

PROTEOMICS: FUNDAMENTALS & TECHNOLOGY PLATFORM

Co-Sponsored by the UCD Genome Center Proteomics Core

This introductory proteome analysis workshop is designed to expose participants to fundamental technology platforms and current information in the field of proteomics. The course will cover bottom up quantitative and non-quantitative electrospray liquid chromatography tandem mass spectrometry (ESI-LC/MS/MS) and “multidimensional protein identification technology (Mudpit LC/LC/MS/MS)” based proteomics using complex mixtures of proteins. Participants will perform in-gel digestions, phosphopeptide enrichment, identification, and database searching using open source software such as X! Tandem and OMSSA with MS/MS data generated during the course. Lectures will cover: fundamentals of protein chemistry and mass spectrometry (MS), MS based protein identification, posttranslational modification of proteins, label free methods of protein quantitation, database searching using MS/MS data, and traditional tools of protein biochemistry. Mass spectrometry and computer lab sessions will include hands on practical applications of the techniques, using state of the art instrumentation and software. Specific course topics may change due to sample and mass spectrometer availability

Dr. Phinney has taught similar Proteomic courses at Cold Spring Harbor in New York.

Lead Instructor:  Brett Phinney, PhD, (UC Davis Proteomics Facility www.proteomics.ucdavis.edu , UC Davis Genome Center). 

Lab Instructors: Rich Eigenheer, Ph.D, Kerry Nugent (Michrom Bioresources), Barrett Smith & Rudy Alvarado

Enrollment is limited to 25 lecture/lab participants and 30 lecture only participants. Register through UCD Conference & Event Services at: http://conferences.ucdavis.edu/proteomics

See schedule of course here

See general info. here

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Next Generation DNA Sequencing Data Analysis For Genome Wide Research

A Bioinformatics Intensive Short Course

Co-Sponsored by the UC Davis Bioinformatics Core and the Genome Center

Next generation sequencing technology is touted as the next wave of the genomics revolution.  The capability to generate tens of millions of sequence reads in a short time and at low cost is stimulating a large array of innovative ways to investigate genome-wide questions.  This course introduces the most popular next generation technologies, including Roche 454 sequencing and the Illumina Genome Analyzer, or Solexa sequencing.  It also provides hand-on training in data analysis pertinent to these two platforms.  Topics include understanding the basics of technology, associated Information Technology (IT) challenges, de novo sequence assembly, mapping to a reference genome, SNP discovery with or without a reference genome, ChIP-seq (Chromatin immunoprecipitation – sequencing) analysis, gene expression, gene predictions, functional annotation, data analysis using the UCSC genome browser, and cluster computing.

Enrollment is limited to 30 students. Register through UCD Conference & Event Services at: http://www.conferences.ucdavis.edu/bioinformatics

See schedule of course

See general info. here

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DNA MICROARRAYS: THEORY, TECHNIQUES AND ANALYSIS

Co-Sponsored by DNA Microarray Core Facility and Affymetrix, Inc.

This hands-on course is a must for any researcher who wants explore the global analysis of gene expression through DNA microarray analysis.  Lectures will be presented by industry scientists as well as academic researchers on the basics of chip technology, including analysis and quality control, and application of this technology in a wide range of research fields.  The laboratory sessions will include preparation of cDNA from RNA, DNA hybridization to and processing of the microchip.  Computer laboratory sessions will include data analysis with clustering as well as other bioinformatics tools.

ADVANCED PCR TECHNIQUES: QUANTITATIVE REAL-TIME PCR

Co-sponsored by the Lucy Whittier Molecular Core Facility

This very popular course covers sampling strategies to obtain high quality sample material, micro-dissection of frozen or paraffin embedded tissues using the new state-of–the art PALM Laser Catapult (Zeiss, PALM Microlaser Technologies), sample preparation and nucleic acid recovery from tissue, blood and paraffin samples, quality controls for sample preparation, and real-time TaqMan PCR and contamination control and monitoring. Students can work on their own samples, including micro-dissection of frozen or paraffin embedded tissues, RNA extraction, QC and gene profiling.