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Illumina Instructor-led Training Courses

Illumina Instructor-led Training Courses


Course Name
GoldenGate Genotyping: An Introduction GoldenGate Genotyping: Best Practices and Troubleshooting Infinium Assay: An Introduction Genotyping Infinium Assay: Best Practices and Troubleshooting Infinium Advanced: Genome-Wide Association Studies (GWAS) Infinium Advanced: Copy Number Variation (CNV) Infinium Advanced: Methylation GAIIx: An Introduction HiSeq 2000: An Introduction MiSeq : An Introduction Sequencing: Advanced Troubleshooting & Best Practices TruSeq DNA Sample Preparation TruSeq RNA Sample Preparation TruSeq Small RNA Sample Preparation TruSeq Exome Enrichment Sample Preparation Library Validation and Quality Control Data Analysis: Intermediate Analysis for Illumina Sequencer Users MiSeq: Experimental Design and Data Analysis Fundamentals

Catalog Number
TR-102-0002 TR-102-0003 TR-103-0001 TR-103-0002 TR-103-0003 TR-103-0004 TR-103-0005 TR-202-0001 TR-202-0002 TR-202-0003 TR-202-0004 TR-203-0001 TR-203-0002 TR-203-0003 TR-203-0004 TR-203-0005 TR-302-0001 TR-302-0002

Sequencing

Sample Prep

Data Analysis

Course Descriptions
Genotyping Courses
GoldenGate Genotyping: An Introduction This introductory course is designed to provide new users a thorough hands-on introduction to the GoldenGate Genotyping assay, including all essential steps in the protocol, sample and BeadChip preparation, sample scanning using a HiScan system, and primary data evaluation and analysis using GenomeStudio software. At the end of this course, participants will be able to effectively perform all the tasks necessary to perform the GoldenGate assay and generate accurate data for genotyping studies. Key Topics & Related Learning Activities: GoldenGate chemistry overview Lab setup, supplies, and support equipment GoldenGate protocol steps and best practice recommendations Assay Design Tool (ADT) features and tasks GenomeStudio features and essential analysis tools Analyzing genotyping and non-genotyping assays that utilize GoldenGate Chemistry

20 April 2012

Illumina Instructor-led Training Courses

Course Number: TR-102-0002 Course Duration: 3 days List Price: $5000 Course Dates: 26-28 Jun 2012, 27-29 Nov 2012 GoldenGate Genotyping: Best Practices and Troubleshooting This intermediate course is designed to provide experienced users with extensive best practice and troubleshooting guidance covering a broad range of potential issues related to the GoldenGate Genotyping Assay. In addition to sample quantification and contamination prevention recommendations, participants also receive instruction on sample and SNP quality control metrics using GenomeStudio analysis software. Key Topics & Related Learning Activities: Sample quantification Use of replicates Contamination prevention Analyzing GoldenGate assay data - Evaluating sample metrics - Evaluating SNP metrics - Evaluating and editing SNP positions Identifying and troubleshooting common GoldenGate failure modes Course Number: TR-102-0003 Course Duration: 2 days List Price: $2800 Course Dates: 29-30 Aug 2012 Infinium Assay: An Introduction This introductory course is designed to familiarize new users with the Infinium Assay through detailed hands-on instruction. Participants will learn all essential steps in the Infinium protocol, including sample and BeadChip preparation, sample scanning using the HiScan system, and primary data evaluation and analysis using GenomeStudio software. Key Topics and Related Learning Activities: Introduction and review of the Infinium Assay and related controls Infinium assay lab setup and preparation Infinium protocol steps and best practices HiScan system setup and operation GenomeStudio software features, operation, and standard reports Course Number: TR-103-0001 Course Duration: 3 days List Price: $3900 Course Dates: 24-26 Apr 2012, 7-9 Aug 2012, 25-27 Sep 2012 Infinium Assay: Best Practices and Troubleshooting This intermediate course provides experienced users with extensive guidance on how to identify and troubleshoot errors that can arise when performing the Infinium assay. A detailed review of best practices for optimizing performance of the Infinium assay is also provided. Key Topics and Related Learning Activities: Infinium chemistry and internal controls GenomeStudio feature review Identifying and troubleshooting common Infinium assay failure modes

20 April 2012

Illumina Instructor-led Training Courses

Course Number: TR-103-0002 Course Duration: 2 days List Price: $2800 Course Dates: 15-16 May 2012, 5-6 Jun 2012, 19-20 Jun 2012, 10-11 Jul 2012, 24-25 Jul 2012, 14-15 Aug 2012, 11-12 Sep 2012, 6-7 Nov 2012, 11-12 Dec 2012 Infinium Advanced: Genome-Wide Association Studies (GWAS) This advanced course provides best-practice guidance on optimizing the Infinium assay for genome-wide association studies (GWAS). Participants will learn how to use a broad range of analysis tools, including those in GenomeStudio software. Upon completion of this course participants will be able to download control data from iControlDB, assess data quality, and understand the workflow for performing analyses to determine significant GWAS study outcomes. Key Topics & Related Learning Activities: Review of Infinium High Density (HD) or Long Capillary Gap (LCG) Assays Genotyping controls and the Illumina Genome Viewer (IGV) - Sample dependent controls - Sample independent controls - Using B allele frequency (BAF) and LRR to evaluate sample quality GWAS Data Analysis Workflow Overview - Quality control (QC) of GWAS data within GenomeStudio - Overview of GWAS data QC outside of GenomeStudio Integration of Illumina GWAS data with analysis tools downstream of GenomeStudio Increasing sample size by using iControlDB (Note: It is highly recommended that participants in this course also complete the Infinium Assay: Best Practices and Troubleshooting Course prior to attending.) Course Number: TR-103-0003 Course Duration: 1 day List Price: $1500 Course Dates: 17 May 2012, 12 Jul 2012, 13 Sep 2012 Infinium Advanced: Copy Number Variation (CNV) This advanced course provides detailed guidance for optimizing the Infinium Assay on highdensity BeadChips for CNV or Cytogenetic analysis. An overview of Infinium products optimal for CNV studies will be presented, along with a review of best practices for CNV analysis. Upon completion of this course, participants will be able to perform quality control tasks on CNV study data, as well as perform advanced analyses using tools in the GenomeStudio and Karyostudio data analysis applications. Key Topics and Related Learning Activities: Review of Infinium High Density (HD) or Long Capillary Gap (LCG) workflows Genotyping controls and the Illumina Genome Viewer (IGV) - Sample dependent controls - Sample independent controls - Using BAF and LRR to evaluate sample quality Genotyping data analysis - GenomeStudio analytic tools and features - Quality control of data in GenomeStudio - CNV analysis within GenomeStudio Downstream analysis tools (12 tools presented) (Note: It is highly recommended that participants in this course also complete the Infinium Assay: Best Practices and Troubleshooting Course prior to attending.)

20 April 2012

Illumina Instructor-led Training Courses

Course Number: TR-103-0004 Course Duration: 1 day List Price: $1500 Course Dates: 21 June 2012, 26 Jul 2012, 8 Nov 2012 Infinium Advanced: Methylation This advanced course offers experienced users best practice guidance on the Infinium Methylation protocol and reviews numerous analysis tools in GenomeStudio software for evaluating study data. Participants work through exercises using methylation and differential methylation analysis. Key Topics and Related Learning Activities: Infinium methylation assay workflow review and best practices Methylation controls - Bisulfite conversion - Specificity controls - Negative controls - Normalization controls QC of Methylation data in GenomeStudio - Background subtraction - Normalization options - Detected genes - Housekeeping genes Methylation Data Analysis - GenomeStudio data analysis review - Advanced methylation analysis tools - Creating clusters and generating heat maps - Choosing an appropriate cutoff Review of Downstream Analysis Tools (Note: It is highly recommended that participants in this course also complete the Infinium Assay: Best Practices and Troubleshooting Course prior to attending.) Course Number: TR-103-0005 Course Duration: 1 day List Price: $1500 Course Dates: 7 Jun 2012, 16 Aug 2012, 13 Dec 2012

Sequencing Courses
GAIIx: An Introduction This introductory course provides new users comprehensive instruction on library preparation and setup, operation, and maintenance of the Genome AnalyzerIIx (GAIIx) system. Upon completion of this course, participants will be able to efficiently perform all tasks necessary to achieve successful runs on a GAIIx. Key Topics & Related Learning Activities: Introduction to the GAIIx System - Overview of the sequencing workflow - Overview of the library preparation process - Overview of GA system and theory of operations Cluster Preparation on cBot (hands-on) - Reagent preparation - Library preparation

20 April 2012

Illumina Instructor-led Training Courses

- cBot wash - Starting the clustering process Setting up and performing a GAIIx Run (hands-on) - GA tour and wash - Reagent preparation, loading and priming - Loading a flow cell - Starting a run using Sequencing Control Software (SCS) - Reviewing first base report - Paired-end run preparation, loading and priming Monitoring a run with the Sequence Analysis Viewer GA system customer resources cBot and GA systems maintenance and best practices Overview GA data analysis Basic cBot and GA troubleshooting Course Number: TR-202-0001 Course Duration: 3 days List Price: $3900 Course Dates: 15-17 May 2012, 21-23 Aug 2012, 4-6 Dec 2012 HiSeq 2000: An Introduction This introductory course provides new users with instruction in library preparation, setup, operation, basic troubleshooting, and maintenance of the HiSeq 2000 system. Hands-on training includes cluster generation using the cBot clustering instrument, and initiating and monitoring a paired-end sequencing run. Key Topics and Related Learning Activities: HiSeq system introduction - Overview of sequencing workflow - Library preparation process review - HiSeq sequencing system overview and theory of operations Cluster Preparation (hands-on) Setting up and performing a HiSeq run (hands-on) - HiSeq tour and wash - Reagent preparation, loading and priming - Loading a sample sheet - Starting a run using HiSeq Control Software (HCS) - Reviewing first base report - Paired-end run preparation, loading and priming - Stopping/pausing a run - Setting up a second flow cell - Monitoring a run with the Sequence Analysis Viewer (SAV) Introduction to Illumina Experiment Manager HiSeq System customer resources cBot and HiSeq systems maintenance and best practices Overview HiSeq data analysis Basic cBot and HiSeq troubleshooting Course Number: TR-202-0002 Course Duration: 3 days List Price: $3900 Course Dates: 24-26 Apr 2012, 10-12 Jul 2012, 9-11 Oct 2012

20 April 2012

Illumina Instructor-led Training Courses

MiSeq: An Introduction This hands-on introductory course provides new users essential instruction in the setup, operation, and maintenance of the MiSeq system. By the end of the course, participants will be able to proficiently initiate and monitor a paired-end sequencing run. (Note: Due to time constraints, course participants will not be able to analyze their own samples.) Key Topics and Related Learning Activities: MiSeq System Introduction and Overview - Sequencing workflow - Library preparation process - Run setup Starting a run (hands-on) - Reagent preparation - Library preparation - Loading a sample sheet - Starting a run using MiSeq Control Software (MCS) - System maintenance Monitoring a run on the MiSeq System - MCS features and tools - Using Sequence Analysis Viewer (SAV) Introduction to Illumina Experiment Manager Introduction to MiSeq Reporter Software (MRS) Introduction to BaseSpace MiSeq customer resources Course Number: TR-202-0003 Course Duration: 2 days List Price: $2800 Course Dates: 22-23 May 2012, 1-2 Aug 2012, 31 Oct-1 Nov 2012 Sequencing: Advanced Troubleshooting & Best Practices This advanced course is designed to help experienced users identify and troubleshoot a broad range of issues that can occur in each stage of the Illumina sequencing workflow, covering sample preparation through data analysis. The best practice guidance provided in this course can help even the most proficient users find new time- and cost-saving opportunities. Key Topics & Related Learning Activities: Overview of Illumina sequencing workflow Sample preparation troubleshooting Cluster generation troubleshooting Run start Troubleshooting Run rescue Run Monitoring Troubleshooting Scenarios Data analysis troubleshooting Course Number: TR-202-0004 Course Duration: 2 days List Price: $2800 Course Dates: 12-13 Jun 2012, 26-27 Sep 2012, 12-13 Dec 2012

20 April 2012

Illumina Instructor-led Training Courses

Sample Preparation Courses


TruSeq DNA Sample Preparation This hands-on introductory course provides detailed training on Illuminas TruSeq DNA sample preparation solution. In addition to expert instruction and best practice guidance for performing and troubleshooting the basic protocol, this course also provides invaluable recommendations on library validation and quality control. At the end of this course participants will be able to efficiently and consistently prepare sample libraries for use on Illumina sequencers. Key Topics and Related Learning Activities: Introduction to Illumina sequencing and library preparation Quantification and fragmentation of genomic DNA End repair, adenylation, and ligation Gel size selection and PCR enrichment Checking library quality and using qPCR to accurately quantify libraries Troubleshooting problem libraries Library validation best practices Sample preparation best practices review Analyzing sample quality data Illumina in-line controls Course Number: TR-203-0001 Course Duration: 3 days List Price: $3900 Course Dates: 10-12 Apr 2012, 17-19 Jul 2012, 2-4 Oct 2012 TruSeq RNA Sample Preparation This hands-on introductory course provides detailed training on Illuminas TruSeq RNA sample preparation solution. In addition to expert instruction and best practice guidance for performing and troubleshooting the basic protocol, this course also provides invaluable recommendations on library validation and quality control. At the end of this course participants will be able to efficiently and consistently prepare RNA sample libraries for use on Illumina sequencers. Key Topics and Related Learning Activities: Introduction to Illumina sequencing and library preparation Quality control of input RNA Perform all steps of TruSeq RNA sample preparation Evaluation of library quality and accurately quantify libraries with real-time PCR Analyze sample quality data Sample preparation best practices review Troubleshooting problem libraries Library validation best practices Illumina in-line controls Course Number: TR-203-0002 Course Duration: 3 days List Price: $3900 Course Dates: 12-14 Jun 2012, 31 Jul-2 Aug 2012, 30 Oct-1 Nov 2012 TruSeq Small RNA Sample Preparation This hands-on introductory course provides detailed training on Illuminas TruSeq small RNA sample preparation solution. In addition to expert instruction and best practice guidance for performing and troubleshooting the basic protocol, this course also provides invaluable

20 April 2012

Illumina Instructor-led Training Courses

recommendations on library validation and quality control. At the end of this course participants will be able to efficiently and consistently prepare sample libraries for use on Illumina sequencers. Key Topics and Related Learning Activities: Introduction to Illumina sequencing and library preparation Quality control of input RNA Perform all steps of TruSeq small RNA sample preparation protocol Pool libraries to maximize efficiency and throughput Gel size selection Evaluation of library quality Analyzing sample quality data Sample preparation best practices review Troubleshooting problem libraries Course Number: TR-203-0003 Course Duration: 2 days List Price: $2800 Course Dates: 22-23 May 2012, 18-19 Sep 2012 TruSeq Exome Enrichment Sample Preparation This hands-on introductory course provides detailed training on TruSeq DNA sample preparation paired with TruSeq Exome Enrichment. In addition to expert instruction and best practice guidance for performing and troubleshooting the basic protocols, this course also provides invaluable recommendations on library validation and quality control. At the end of this course participants will be able to efficiently and consistently prepare and enrich sample libraries for use on Illumina sequencers. (Note: Due to the lengthy hybridization steps required, participants will use pre-hybridized DNA libraries to complete the TruSeq Exome Enrichment protocol. This strategy ensures hands-on training with all critical steps, while minimizing redundancy.) Key Topics and Related Learning Activities: Introduction to Illumina library preparation and targeted resequencing Fragmentation of genomic DNA Perform all steps of TruSeq DNA sample preparation using the gel-free method Perform one round of TruSeq Exome Enrichment Evaluation of library quality and quantity Sample preparation best practices review Troubleshooting problem libraries Library validation best practices Illumina in-line controls Course Number: TR-203-0004 Course Duration: 3 days List Price: $3900 Course Dates: 26-28 Jun 2012, 21-23 Aug 2012, 13-15 Nov 2012 Library Validation and Quality Control This course provides valuable best practice guidance to ensure libraries are properly evaluated for quality and quantity prior to sequencing on Illumina sequencers. After reviewing the sample preparation theory and workflows, participants get hands-on training in validating sample libraries using recommended bioanalytical and real-time PCR techniques. Many best practice and troubleshooting tips are provided throughout the course. Applicable portions of this course have also been incorporated in the TruSeq DNA, TruSeq RNA, and Exome Enrichment sample preparation courses. Course Number: TR-203-0005

20 April 2012

Illumina Instructor-led Training Courses

Course Duration: 1 day List Price: $1500 Course Dates: 24 May 2012, 20 Sep 2012, 6 Dec 2012

Data Analysis Courses


Data Analysis: Intermediate Analysis for Illumina Sequencer Users This course is designed for experienced users, providing in-depth instruction on the tools and process used for conducting primary and secondary analysis on data acquired from Illumina sequencers. The primary analysis portion of course covers Real Time Analysis (RTA), the Offline Basecaller (OLB), run folder structure, and image analysis. The secondary analysis portion of the course covers CASAVA tools and de-multiplexing. Course Number: TR-302-0001 Course Duration: 1 day List Price: $1500 Course Dates: 9 May 2012 MiSeq: Experimental Design and Data Analysis Fundamentals This course provides new users a thorough introduction to Illumina sequence data. Participants will learn the most common types of analysis methods, and will have the opportunity to design a MiSeq experiment, analyze the data, and interpret the results. Key Topics and Related Learning Activities: Introduction to Illumina next-generation sequencing data Applications of Illumina sequencing data Key concepts for analyzing next-generation sequencing data - Scale of data sets - Range of complexity - Effective usage of results for scientific inquiry - Genome structure and variation Workflows - De novo assembly - Realignment applications: resequencing, amplicon sequencing, and related applications such as ChIPSeq - Counting applications: small RNA, metagenomics, and related applications such as RNA-Seq Analysis and interpretation of MiSeq data - MiSeq run folder structure and contents - Best practices for using MiSeq Reporter (MSR) to run and re-queue jobs - Navigating and interpreting MSR results - Post-MSR analysis using CASAVA, combining multiple runs, and third party tools Course Number: TR-302-0002 Course Duration: 2 days List Price: $2800 Course Dates: 19-20 Jun 2012

20 April 2012