Hybridization/DATA 1 Workshop

Data1 Presenters: A. Malcolm Campbell, Laurie Heyer, and Johanna Hardin; Hybridization presenters: Laura L. Mays Hoopes, Anne Rosenwald, Todd Eckdahl, Mark Salata, Mary Lee Ledbetter

 

Welcome to the GCAT workshop on Microarray Data Analysis, section 1 along with Hybridization laboratory experience.  In this workshop, you will learn some ways to teach and learn about microarrays and you will try out techniques for acquiring data, clustering data, and determining statistical significance of differences; then you will prepare labeled cDNA, hybridize it with microarrays, scan the slides, and analyze your own data. 

 

You may check into Copley Hall dorm (see maps on the Georgetown University web site) any time after 4PM on Monday, July 5. 


We hope you have configured any laptop computer that you want to use in advance (for directions, please see "computers" on the main web page for the workshop) but we recognize that not everyone has had time to do that.  If you did not bring a computer, do not worry; a number of computers preloaded with the software will be available for use during the workshop.

 

In most of the activities below, the hybridization workshop and the DATA1 workshop will work together; items in bold for Tuesday afternoon and Wednesday are times when Hybridization has a separate planning or activity meeting in a different location.

 

Tuesday, July 6

8:00 AM  ICC107.  Computer configuration period; bring your lap top computer if you  brought one that you want to use, and the data team will help you get the right configuration and software loaded for the workshop.  Leader: Laurie Heyer, Davidson College. 

9:00 AM Introduction to Microarray Data  (A. Malcolm Campbell,

Davidson College, GCAT Director)

9:45 Introduction to MagicTool  (Laurie Heyer, Davidson College)

10:00 Working with Images and Gene Lists in MagicTool  (Laurie Heyer)

10:30 Break

10:45 Creating Expression Files in MagicTool  (Laurie Heyer)

11:30 Managing Expression Data in MagicTool  (Laurie Heyer)

12:00 lunch break

1:00 Exploring and Clustering in MagicTool  (Laurie Heyer)

2:30  Break

2:45  Statistical analysis/introductory data sets.  (Jo Hardin, Pomona College)

4:00  Begin to work with data set, trying out methods presented.  Please work in

pairs sharing a computer.  (Laurie Heyer/Jo Hardin)

5:00 ICC 103. Go over the plans for cDNA labeling for tomorrow

morning. Laura Hoopes.

 

6:00  Dinner.

 

8:30  Optional Mac software workshop, Malcolm Campbell, Copley

residence hall lounge.

 

Wednesday, July 7  

8:00 AM.  Reiss Laboratory Room 439.

    Working in pairs, Set up cDNA reverse transcription reaction. When incubating,

        return to data analysis. Laura Hoopes (lead instructor), Anne Rosenwald, Todd

          Eckdahl, Malcolm Campbell, Mary Lee Ledbetter, Mark Salata (Hyb

        team).

9:00 AM ICC 103.  Recap of analytical tools/data sets; discussion of experiences in first   

        work period; questions/answers re data analysis startegies and methods. 

        Discussion leader: Jo Hardin.

9:30-11.45  Continue to work with data sets and methods.  Hardin, Heyer

11:30, Reiss Laboratory Room 439/428. 

Discussion of the purification of cDNA and setting up hybridizations.  Laura Hoopes.

12:00 lunch

1:00 Reiss 439/428. Begin purifying the labeled cDNAs, and

continue procedure until the two labeled cDNAs are loaded

onto the hybridization slide and it is incubating.  Leader: Rosenwald;  Hyb

team.

3:30-5:30 As time permits instructors will organize discussion

of course plans of the participants.  Participants have been paired so that course plans are similar, if possible. Lead discussant: Salata.

6:00 dinner. 

8:00 Copley lounge.  Discussion of course plans with individual participants,

        continued. All 8 instructors. Lead discussant: Ledbetter.

 

Thursday, July 8

8:00 AM Reiss laboratory, Room 439/428.

Discussion of procedures to stop hybridization reactions and wash and dry

slides for scanning. Laura Hoopes.

8:30 Take out hybridization, wash and dry slide.

9:30 Small groups will observe the scanning of the slides; the

TA will take each group in turn to observe this process.

9:30 (When not seeing the scanning). Continue to work on

course plans, preparing for presentation to the whole

group on Friday. Lead instructor: Anne Rosenwald. 

10:30 break

10:45 ICC 115. Consultations on how data will be analyzed, on

an individual team basis. Hyb team instructors except for

Campbell. Lead instructor: Todd Eckdahl.

12:00 Lunch break.

1:00 ICC 115. Work in pairs, each pair sharing one computer,

and analyze data from the microarray experiment.  Grid

your own slide using MAGIC Tool. Collect intensity data. 

Othersí intensity data will be made available to import

so you can do comparisons. You may also wish to compare

with DeRisiís own data and with the data from the first

Best Practices Workshop. Hyb team and Data team.  Lead

instructor: Mary Lee Ledbetter.

3:30 Break.

3:45 Continue data analysis and/or planning your own class

methods on microarrays. Hyb team/data team; lead instructor: Anne Rosenwald.

4:45 Panel discussion of ways the instructors have used arrays

in their classes, Q/A re microarrays for undergraduates.

Hyb team instructors. Lead discussant: Mary Lee Ledbetter.

6:00 dinner

7:30 another round of the Mac software optional workshop if needed; Malcolm

        Campbell

 

Friday, July 9.  If leaving today, please check out of dorm by 10:00 AM. 

9:00 AM Reiss 264 classroom.  Continued data analysis and continued planning for

          each participantís uses in class.  Hyb team.  Lead instructor: Mark Salata.

10:00 Reiss 264.  Participants present individual plans to group in 5 minute time    

          slots. At the end of all presentations will be a time for discussions and

suggestions.  Organizer: Laura Hoopes.

11:00 break

11:15 Continued presentations, followed by discussion (both general and specific).    

        Organizer: Laura Hoopes.

11:45 Evaluations of workshop if not going to TIGR

12:00 lunch

1:00 bus to TIGR to hear talks on how microarrays are being

used today in cutting edge research

4:00 bus back to Georgetown University

6:00 evaluation of workshop; dinner

 

depart, or stay tonight and depart tomorrow morning by previous arrangement, checking out before 10 AM.