This course contains narrated presentations and video-based lab modules from the Genome Analyzer Boot Camp developed jointly by The Broad Institute and Illumina and held in February 2010. In this online version of the Boot Camp sessions, you’ll get an in-depth look at the chemistry and workflows for the Genome Analyzer. You’ll learn tips and tricks as well as best practices developed by the Broad to achieve even higher performance from the Illumina Genome Analyzer.
This course is intended for technician-level individuals who have some wet lab experience with the Illumina Genome Analyzer and corresponding sample prep techniques. The video sessions will take approximately 3 hours 25 minutes to complete.
We welcome any feedback on the course, and would also love to hear about the things that you are doing in your labs! For more information about GA Boot Camp, or to provide feedback, please email gabootcamp@broadinstitute.org.
Course Content
| Sample Prep | ||
| Videos and Slides | View | Download |
| Illumina – Sample Preparation (Chemistry) | [ video ] | [ slides ] |
| Broad – Sample Preparation (Tracking, Shearing, Diversity, Size Selection, SPRI) | [ video ] | |
| Lab 1a Video | [ video ] | |
| Lab 1b Video | [ video ] | |
| Posters (from Lab 1a Video) | ||
| Agilent Bioanalyzer considerations | [ poster ] | |
| Effects of Covaris Shearing Factorial settings | [ poster ] | |
| Cluster Generation | ||
| Videos and Slides | ||
| Illumina – Cluster Generation (Chemistry) | [ video ] | [ slides ] |
| Broad – Cluster Generation (QPCR, Controls, SYBR QC) | [ video ] | |
| Lab 2 Video | [ video ] | |
| Sequencing | ||
| Videos and Slides | ||
| Illumina – Sequencing (Chemistry) | [ video ] | [ slides ] |
| Broad – Sequencing (Workflow, 1st base, Failure Mode Gallery) | [ video ] | |
| Lab 3a Video | [ video ] | |
| Lab 3b Video | [ video ] | |
| Illustrations (from Lab 3a Video) | ||
| Sequencer stage set-up |
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| Data Analysis | ||
| Videos and Slides | ||
| Illumina – Working with Data (Pipeline workflow) | [ video ] | [ slides ] |
| Broad – Working with Data (Troubleshooting, Data files, Concepts) | [ video ] | |
| Lists and Data Process Map | ||
| List of Acceptable Metrics | [ list ] | |
| Troubleshooting Data Process Map | [ map ] | |
| List of File Locations | [ list ] | |
Presenters:
Sample Prep: Karen Israel, Maura Costello, Laura Lambiase, Purnima Kompella, Brian Minie, Jillian Nolan
Cluster Generation: Karen Israel, Tim Desmet, Matt Coole, Laurie Holmes, Adam Navidi
Sequencing: Klaus Ullman, Sheridon Channer, Amy Biasella, Dalin Chan, Paul Frere, Sheridon Channer, Mike Monahan
Data Analysis: Klaus Ullman, Kristen Connolly, Amy Biasella, Jim Meldrim
