Joining GCAT costs nothing if you do not want to use DNA microarrays from GCAT or use a GCAT scanner. To join, the best place to start is signing up for the listserv called GCAT-L. This is how all GCAT communication begins, including the time when requests for microarrays are being accepted. You might want to attend a free GCAT workshop to learn how to perform experiments and analyze data.

 

GCAT tries to obtain microarrays for these species:

• Yeast (S. cerevisiae; Washinton Univ., St. Louis)
• Yeast bar code microarrays (No Longer Available)
• E. coli (University of Alberta)
• Arabidopsis (Univ. AZ) Only 31 available, first come first served
• Chlamydomonas (Stanford Univ.) No Longer Available
• Maize (Univ. AZ) No more requests, all chips pre-ordered
• soy beans (Univ. of Illinois) All requests due by April 29, 2011
• tomato (Cornell Univ.) Only 53 available, first come first served
• rice (Univ. AZ) No more requests, all chips pre-ordered
  
• Mouse (Washinton Univ., St. Louis)
• Rat (Washinton Univ., St. Louis)
• Human (Phalanx Biotech Group)
• Fly (D. melanogaster; Univ. Health Network, Toronto)
• C. elegans (Washinton Univ., St. Louis) No Longer Available
• Chicken (Univ. AZ)
• zebra fish (Agilent) No Longer Available

Due to GCAT's recent HHMI support, we will be able to produce our own yeast microarrays! All other species will continue to be supplied by academic labs, though now GCAT will be able to compensate the labs for their generosity. Since we obtain most microarrays from labs that have their own research interests, we cannot guarantee non-yeast species or number of microarrays. However, GCAT always tries to meet the needs of its members.

Pricing Structure and Availability

A) Schools supporting GCAT with their HHMI money will get first options and will not need to pay any more money to obtain the microarrays.

B) All other schools will need to pay the standard rate of $60 for the first microarray and $20 for each additional microarray, per semester. $40 dollars covers FedEx shipping and packaging. The $20 was mandated by NSF and pays for the scanner's service contract. Malcolm does not receive any compensation for this work, nor does Davidson College. We can only accept checks.

C) I will do my best to match all requests, but for non-yeast microarrays, there may be a limitation to the number of microarrays any one school can receive through GCAT.

D) The species we have available this coming year are:

• • Yeast (S. cerevisiae; Washinton Univ., St. Louis)
  • Yeast bar code microarrays (No Longer Available)
  • E. coli (University of Alberta)
  • Arabidopsis (Univ. AZ) Only 31 available, first come first served
  • Chlamydomonas (Stanford Univ.) No Longer Available
  • Maize (Univ. AZ) No more requests, all chips pre-ordered
  • soy beans (Univ. of Illinois) All requests due by April 29, 2011
  • tomato (Cornell Univ.) Only 53 available, first come first served
  • rice (Univ. AZ) No more requests, all chips pre-ordered
    
  • Mouse (Washinton Univ., St. Louis)
  • Rat (Washinton Univ., St. Louis)
  • Human (Phalanx Biotech Group)
  • Fly (D. melanogaster; Univ. Health Network, Toronto)
  • C. elegans (Washinton Univ., St. Louis) No Longer Available
  • Chicken (Univ. AZ)
  • zebra fish (Agilent) No Longer Available

E) What do I need now is to hear from you? Tell me what you want using these guidelines.

F) If you have a new species you'd like to work with, then provide Malcolm Campbell with the contact information of a lab you think might be willing to share with GCAT. Malcolm will contact them to see if this species can be added to the list.

G) If your institution requires a W-9 form, please enter this information:

• Check the N - Nonprofit Organization box and enter the TIN# 562161106

GCAT is run by Malcolm Campbell as a service to the undergraduate education community. He has a non-profit status bank account set up in Davidson that handles all the money. Therefore, the only way to accept money is in the form of a check (personal or institutional). Sorry, GCAT cannot accept Purchase Orders (PO's) or credit cards. Make checks payable to:

GCAT
c/o Malcolm Campbell
Biology Dept.
Box 7118
Davidson College
Davidson, NC 28035

 

Store your microarrays at room temperature in a dessicator.

 

This is a good question. The money ($60 for the first microarray per species + $20 for each additional microarray) pays for the FedEx delivery of the microarray and the scanning. The GCAT scanner was purchased on an NSF grant where GCAT promised to charge $20 per scan to pay for the service contract (currently $7,000 a year). Malcolm Campbell does not receive any compensation for his services, nor does Davidson College. All money is used for GCAT expenses.

 

You need the following equipment:

• Standard molecular biology small equipment
• Incubation chamber (water or air)
• Compressed air or centrifuge that holds 50 mL conical tubes to dry the slides
• Capacity to isolate and manipulate RNA (many choices of methods)
• cDNA production and labeling kit (many choices but special discounts on 3DNA)
• Access to FedEx or UPS next morning delivery (if you want GCAT to scan your chips)
• Computer with at least 512 MB RAM
• To run GeneSpring or Scanalyze, you need a PC: to run MAGIC Tool, you can use Linux, PC or Mac OSX
• Access to FTP program and the internet.
• Undergraduate students only - no graduate students for wet lab or GeneSpring.

First, you must contact a GCAT scanning center one week in advance to verify the time is acceptable. You must inform the scan center how many microarrays you intend to send and what type of microarrays you are sending. Keep in mind that each microarray takes approximately 30 minutes to scan, so it is helpful to space out your microarrays rather than sending more than 5 at a time.

When you pay $20 per microarray, you have paid for the scanning service. If you obtain your own microarrays but want GCAT to scan them, the charge is $20 per scan. GCAT only scans microarrays for undergraduate research or course work.

You must overnight express by FedEx, UPS, DHL, etc. (not US Mail) your microarrays to GCAT. Do not send them by standard overnight delivery because they arrive too late in the day to scan them on the same day.

Scan Centers:

Your scanned slides will appear on the ISB FTP server. To access the files, you need to use an FTP program, not a web browser. This means you CANNOT use Internet Explorer, or Netscape, or Safari, or FireFox, etc. You must use a program such as Fetch, CuteFTP, CyberDuck, etc.

The URL is ftp.systemsbiology.net. The usrname=gcat (use only lower case letters; see example below). The password will be sent to you by email from Malcolm Campbell after you request it. You will have two tiff files for each scanned slide. To learn more about the tiff file format, go to this web site.

It is very important that you do NOT give the username and password combination out to any students. GCAT is a guest on the ISB server and we do not want to abuse this privilege.

9) What additional information do I need?

You must be able to identify the gene located at each spot (feature). For this, you need to know how the microarray was printed (e.g. how many rows and columns per grid, how many different grids, how many metagrids, how many times each gene was spotted and were gene spots printed in adjacent pairs?). You will also need the genelist or godlist which is a tab delimited text file (or converted to one via Excel) that lists each gene on a separate line. This information must be supplied to you and you can find most of this information at the GCAT Protocols page. Orientation is also an issue which you can learn about on this gridding page.

10) How do I analyze the results? Can you show me a couple outcomes from microarray studies? What are the capabilities of microarrays?

GCAT does not require you to use any particular method. Some faculty prefer Scanalyze to quantify the spots and GeneSpring to analyze multiple microarray data. Scanalyze is free but only works on a PC. GeneSpring has been free and also requires a PC. Each year, GCAT has to negotiate the availability of GeneSpring.

You may want to use MAGIC Tool which was written by GCAT faculty and students and performs both halves of the analysis, though with no bells and whistles. MAGIC Tool works on Linux, PC and Mac OSX.

 

You did not mix the hybe solution well before incubating. Read the Tips File for details.

This problem has a few causes. One is too much SDS that did not get washed off. Other reasons include poor blocking or too little heat while washing. Read the Tips File for details.

 

The most common problem is poor quality RNA. It is easy to degrade. The second most common problem is poor cDNA synthesis. Finally, it helps to boil the microarray before hybridizing. This is required if you are using cDNA (PCR product) spotted on the microarray. Read the Tips File for details.

 

The microarray scanner at Davidson is not laser based. The out of focus blobs (typically circles) are dust spects on the back side (non-DNA side) of your microarray. All microarrays are blown clean with compressed gas, but some dust does not come off. Therefore, it is especially important to use clean wash solutions, do not expose your microarrays to lent-causing fabric such as kimwipes, and keep your microarrasy in a dust-free box.

The scanner at Pomona is laser based and thus does not produce the same spots. However, each device has its tradeoffs, so neither one is perfect.

 

All microarray scans are tiff files and all tiff files are grayscale. The colors you see are generated by the software once you tell the software which file is supposed to be red or green. Each pixel on the tiff file can have a grayscale intensity of 1-128. This information is used by the software to produce the numerical values and the color intensity.

 

If you want your students' data posted too, just email Malcolm Campbell with the URL and the description you want associated with the link.

 

Yes, email Malcolm Campbell with the URL and the description you want associated with the link.

 

You can help in many ways. First, participate in the GCAT-L listserv. When someone asks a question that you can answer, please reply to the list (GCAT-L@davidson.edu) with your answer. "It takes a community to hybe a chip."

Second, you can send URLs for course sites and student data for posting on GCAT.

Third, you can share any presentations your students make by emailing Malcolm Campbell with the details and the description you want associated with the information. GCAT would be happy to mirror any PowerPoint files you care to share.

Fourth, you can send jpeg files for inclusion in our photo gallary of GCAT students and faculty. Your photo can be fun or more serious; your choice.

Fifth, you can volunteer to help coordinate a species. By that, you might act as the go-to person for species-specific questions, help communicate with the microarray supplier, etc.

Finally, you can cite GCAT in any publications or lab manuals you produce. GCAT is an all volunteer organization and we grow through your efforts at communicating success and lesssons learned along the way.

GCAT has offered two hands-on workshops so far, though no others are planned at this time. You should check with Cold Spring Harbor's Dolan DNA Learning Center. There have been two MAGIC Tool workshops as well.

20) Are there non-RNA methods I could use instead?

Yes, there are two options. One is comparative genome hybridizations where you label genomic DNA instead of cDNA. This allows you to compare two similar species or strains, or mutant and wild-type isolates. Do a PubMed search to learn more. Here is one example.

Malcolm Campbell has also developed some "teaching chips" which use oligonucleotides as probes and cloned PCR products as spotted targets. You could produce these "microarrays" by hand if you wanted.

 

Yes, GCAT has several tiff files and expression files you can use to get started on dry lab data analysis. GCAT is also collaborating with Cybertory.org as they continue to develop their synthetic tiff file production method.

Yes, lots of them. A good starting place is Stanford Microarray Database, but you can find many others through PubMed. You might also check out the Open Accesss journal PLoS.

 

This is a multiple choice question:

24) GCAT looks interesting, but I have no idea how to proceed. Where do I start?

First, sign up for GCAT-L listserv. This will keep you informed on the news and what problems people are working on. Once a year, a call goes out for microarray requests. You must submit your request by the stated deadline in order to be considered for microarrays in the coming academic year. Because GCAT is an all volunteer organization, we cannot take requests year round.

Second, you can begin with dry-lab experiments. You can use MAGIC Tool and analyze the practice data or download real data sets online.

It turns out that the hard part is not collecting data (though that's not easy), the hard part is data analysis. So you can start there for free and see how it goes.