| Home | Class
Calendar |
Reading List |
Resource Links | Problem Sets |
|
Date
|
Session
|
Topics
|
Assigned
Reading (see Reading List page for links) |
| April 4, Wed |
Course Overview |
Administrative issues, background, goals, overview of course |
|
| April 6, Fri |
Cancelled |
||
| Apr 9, Mon |
Lecture Introduction |
Vocabulary Basic types of DNA arrays: Spotted oligo/cDNA, Affymetrix Oligos v. PCR products v. In situ oligo synthesis Types of Array Experiments |
Text: Chapters 1 & 2.4, Lockhart Nature review |
| Apr 11, Wed |
Lecture Introduction 2 |
Alternate Array platforms Types of Data Analysis Limitations of Arrays |
Text: Rest of Chapter 2, Eisen Methods in Enzymology review |
| Apr 13, Fri |
Paper Discussion |
Classic Yeast Papers |
Spellman Yeast Cell Cycle paper, Gasch Environmental Stress paper |
| Apr 16, Mon |
Lecture Spotted Array Design |
Oligo v. PCR product arrays Resources for making a spotting robot |
Text Chapter 3 |
| Apr 18, Wed |
Lecture Types of Experiments / Databases |
Types of Experiments Choices of References Microarray Databases |
Text Chapter 4 |
| Apr 20, Fri |
Paper Discussion |
Compendiums of array experiments |
Hughes,
Cell 2000 compendium
paper Scherf, Nat Genetics 2000 molecular pharmacology of cancer paper |
| Apr 23, Mon |
Lab 1 |
GenePix Introductory Lab Gridding Data Extraction Using a Print-list |
GenePix Manual, chapters 1-4 [Download GenePix Software] |
| Apr 25, Wed |
Lecture | Normalization |
|
| Apr 27, Fri |
Paper Discussion | Ammonium toxicity & use of chemostats in yeast |
Hess
et al., PLoS Biology, 2006 Ammonium toxicity paper |
| Apr 30, Mon |
Lab 2 |
Bioconductor &
normalization |
|
| May 2, Wed |
Lecture | Cancelled -rescheduled for May 3
makeup |
|
| May 4, Fri |
Paper Discussion | Cross-platform reproducibility
of array data |
See Reading List |
| May 7, Mon |
Lab 3 |
More Normalization For May 10: Cluster Analysis |
Using Cluster and TreeView |
| May 9, Wed |
Lecture | Normalization |
|
| May 11,Fri |
Lecture
on Clustering More Clustering Lab |
Clustering |
|
| May 14, Mon |
Paper Discussion |
||
| May 16, Wed |
Lecture | Finding significant gene
expression changes Integrating microarray data with genomic data to find transcription control regions |
|
| May 17 Thurs |
Lab 4 |
Using Microarray Web Resources: Analysis: CARMAWeb Data Retreival: Geo, Gene Xpress Databases |
|
| May 18, Fri |
Paper Discussion | Evolution of Gene Expression | Khaitovich review Gilad et al., Evolution of transcription factor expression |
| May 21, Mon |
Lab 5 Guest Instructors |
Using ClueGene |
|
| May 23, Wed |
Group Presentation Lab (Wed-Thurs group) |
Group Presentation: Grant &
Hongqing Wed-Thurs Lab Group: Meet at 8:30am in 134 to start hybridizing arrays |
|
| May 24, Thurs |
Lab 6 |
Wed-Thurs Group: Meet at 8:30am
to wash & scan arrays Thurs-Fri Groups: Meet at 10am in Baskin 134 to hybridize arrays |
|
| May 25, Fri |
Lab |
Thurs-Fri Groups: Meet at 10am
to wash & scan your arrays |
|
| May 28, Mon |
Holiday |
No class |
|
| May 30, Wed |
Group Presentation |
Pinal & Rachel |
|
| May 31 Thurs |
Lab Time |
Work on analyzing your array
data from last week |
|
| Jun 1, Fri |
Group Presentation |
John & Marcos |
|
| Jun 4, Mon |
Group Presentation |
Nick & Kivanc | |
| Jun 6, Wed |
Group Presentation |
Greg & Navya |
|
| Jun 8, Fri |
Group Presentation |
Jonathan & Dan |
|
| Jun 14, Thurs |
Pseudo-grant & your array
data analysis due 5pm |