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A Leisurely Look at Genomic Research Using Microarrays-Winter 2004
FRS 001T -- Sec. 001 -- (1 unit) -- CRN 35580 -- R 5:10-6:00 PM--25 Wellman
Course Description
Instructor: Danh Nguyen
Office: TB 169
Office hours: By appointment.
Email: ucdnguyen@ucdavis.edu
Course Outline:
Week 1: Introduction to the basics. Cells, genes, genome, proteome, transcriptomics.
Read "genetics 101"
(Sections: a. From gene to proteome, b. What we've learned so far, c. The next step: functional genomics.
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
Review basic molecular biology
figures 2, 3, 4, and 5.
Week 1 discussion notes [MS Word]
Week 2: 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 discussion notes [MS Word]
Week 3: Introduction to microarrays. Measuring global transcription: Transcriptomics.
Microarray experiments. Two main types of microarray: 1. cDNA and 2. oligonucleotide microarray.
Week 3 discussion notes [MS Word]
Handout (figure) on reverse transcription process.
Week 4 & 5: Review week 3 discussion notes and question posed at the end. Re-read Times article from week 2 and relate to
what has been learned/discussed in class thus far. Do you have any specific comments on the article, now that you have
been presented with the background information/motivation (from class) on microarrays?
In week 4 and 5 we will continue on with:
Discussion of microarray (experimental procedure) and interpretation of microarray
data. Example: using cDNA microarray in cancer reseach.
Cancer classification and diagnostic. Cancer subtype
discovery. Specific examples: B-cell lymphoma
(Nature article, 02/2000),
Acute leukemia
(Science article, 10/1999).
Week 4 handout [MS Word]
Week 4 discussion notes [MS Word] This also contains the
assignment due in class week 5 (2/5/04).
Week 5 discussion notes [MS Word]
Week 6: Discussion of acute leukemia example.
Week 6 discussion notes [MS Word]
Week 7 Break. No class (THURSDAY 2/19/04).
Week 8: Example: microarray and SARS (severe acute respiratory syndrome). Read USA Today article
"Gene chip helps
identify mystery illness" (04/2003).
Read article
Viral discovery and sequence recovery using
DNA microarrays (4 pages; You can skip the "Materials and Methods" section if you want to.)
This will be our main discussion article.
Final summary report. Please write (2-3 pages) summary report of the course. This summary may include
anything on this website, your discussion notes, recollection of our discussions etc. You are welcomed
to use materials beyond this, but it is not required. Have a creative tilte, diagrams, schema, your opinions,
etc. incorporated into this summary. Please let me know if you need more clarification or have questions etc.
Week 9: Last day of class (Thursday 3/04/04). Final discussion.
Final summary report due. Discussion of grades for course.
Week 10: No class (Thursday 3/11/04).
Links: Access Excellence Graphics Gallery
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