Time: MWF 2-3:10pm Location: Lectures: Baskin 372
Computer Labs: Baskin 109Course Info Link: www.soe.ucsc.edu/~lowe/courses/MicroarrayW03/
| Instructor | Todd Lowe |
| lowe@soe | Phone | 459-1511 | Office | 227 Sinsheimer | Office Hours | Wed 3:30-4:30, Thur 2-3pm & by appt. |
| 50% | Problem sets |
| 50% | Final Project - Data Set Analysis Write-up |
| Date | Lecture | Topics |
|---|---|---|
| January 3 | Overview of Course | |
| January 6 | Introduction | Vocabulary
Basic types of DNA arrays: Spotted oligo/cDNA, Affymetrix Oligos v. PCR products v. In situ oligo synthesis Types of Array Experiments |
| January 8 | Introduction II | Types of Data Analysis
Limitations of Arrays Array + Sequence Analysis |
| January 10 | Experimental Design | Time-resolved data
Comparison of different genetic backgrounds Comparison of different developmental stages Cancer/Tumor Classification Comparison of different genomes Human SNP Mapping Spellman Yeast Cell-Cycle Paper (please read before class) |
| January 13 | Spotted DNA Array Design
& Construction |
PCR fragment / Oligo Feature Design
Building a spotting robot Preparing slides Preparing DNA samples Spotting |
| January 15 | Spotted DNA Array Design (cont) Demos |
Post-processing and care of arrays Scanning Demo Spotting Robot Demo |
| January 17 | Lab #1: Using GenePix | GenePix Tutorial
Meet in Kresge computer lab Gridding Data Extraction Using a Print-list |
| January 20 | Holiday - No class | |
| January 22 | Introduction to R and Bioconductor | Guest Lecturer: Andy Pohl |
| January 24 | Using Arrays to Study RNA Processing | Guest Lecturer: Manny Ares |
| January 27 | Lab #2: Introduction to R & Bioconductor | Lab exercise
Meet in Baskin 109 Computer lab |
| January 29 | Microarray Club Guest Lecture: Sandrine Dudoit |
Bioconductor & other cool stuff |
| Basic Analysis | Clustering
Self-organizing maps K-means mRNA expression DNA copy number changes / footprinting Cross-species hybridization |
|
| Advanced Analysis | Singular value decomposition
Support Vector machines Correspondence analysis / Principle component analysis Gene Shaving Cross-Experiment Analyses Identifying regulatory networks, Church et al. Promotor sequence discovery, Gibbs sampling techniques |
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| Other Kinds of Arrays |
Protein arrays Tissue arrays |
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| New Array Technologies |
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