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A Leisurely Look at Genomic Research Using Microarrays-Winter 2008
FRS 001T -- Sec. 007 -- (1 unit) -- CRN 25348 -- Tu 5:10-6:00 PM--25 Wellman
Course Description (TRC)
Instructor: Danh Nguyen, Ph.D.
Office: MS1C RM 149 (direction/map)
Office hours: By appointment.
Email: ucdnguyen@ucdavis.edu
Syllabus [PDF]
Week 1: Genes and gene expression basics.
Read "genetics 101"
(Sections: a. From gene to proteome, b. What we've learned so far, c. The next step: functional genomics.
Please skip the section on "How is genome sequencing done?"). Read pages 3-6 of handout "The Answer in a
Nut Schell: Genes, Proteins, and the Meaning of Life" (chapter 1 from The Human Genome: A User's
Guide by R.S. Hawley and C.A. Mori): pages
3
4
5
6.
Week 2: From genes to genomes.
Introduction to basics continued. Transcriptomics: measuring "all" messenger RNA. Genomics research.
Diagram of cDNA micorarray process.
For next week, read
description of microarray from NHGRI (National Human Genome Research Institute).
Also read Times article
"DNA Microarrays: The workhorse of genomic medicine" by Unmesh Kher (01/2001),
Week 2 handout:
[MS Word format] --
[PDF format]
Assigment 1 (Due week 3 1/22):
[MS Word format]--
[PDF format]
Week 3: More on microarray experimental procedure, gene vs. genomics approach.
We will continue discussion of microarray experimental procedure and genomics approaches.
Application 1: Leukemia classification.
Reading materials for week 3: Science article.
[PDF format]
Week 3 handout:
[MS Word format]
[PDF format]
Week 4:
Application 2: "Discovering" (investigating) subtypes of B-cell lymphoma.
Reading materials: Nature article.
[PDF format]
Reading guide/questions for discussion:
[MS Word format]
[PDF format]
Discussion: Some basic principles of genomics expression analysis
Week 5: Application 3: Infectious diseases, SARS, Bird Flu & microarrays.
Review: cDNA microarray:--Please go through the following cartoon animation of the cDNA microarray process:
cDNA animation.
Review (optional, only if you're interested): Affymetrix (oligo) array: This part is optional,
but if you like please view animation:
here.
Click on View the Animation under "How to Use GeneChip® Microarrays to Study Gene Expression"
Group/individual assignment:
[MS Word format]
[PDF format]
Reading materials for week 5:
Article 1:
[PDF format]
Article 2:
[PDF format]
Article 3:
[PDF format]
Reading materials for week 6:
Article 4:
[PDF format]
Assignment # 3:
[MS Word format]
[PDF format]
Links: Access Excellence Graphics Gallery
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