TIGR Solanaceae Genomics Resource

TIGR Potato cDNA Array FAQs

1. I finished my paperwork but I still do not have my microarrays?

Did you fill out all of the paperwork? Did you fax TIGR the Simple Letter Agreement? Has your institution sent in the payment? TIGR will ship out your microarrays within 30 days after receipt of the completed simple letter agreement and payment. If you are curious about the status of your order, send an email to potato@tigr.org.

2. How do I store the microarrays after I have received them?

You should store the microarrays in a dessicator in the dark slide box they were shipped in.

3. How should I hybridize my RNA to the microarrays?

We enclosed a robust protocol for hybridizations with the materials we sent you. We strongly recommend you use this protocol.

4. Now that I have hybridization results, how can I analyze the data?

A variety of software packages are commercially available for analyzing microarrays. You can use them or obtain a freeware version available from academic institutions or from TIGR (http://www.tigr.org/software).

5. Why are some of the spots on the microarrays listed as "Do not use. Not validated"?

Several steps are involved in making microarrays including selecting clones, growing clones, preparing DNA, sequence verification, PCR amplification, gel analysis and quantitation. The TIGR potato microarrays are done in a high-throughput manner (i.e., microtiter plates of 96 wells). If a well (clone,element) fails for any of the above reasons, the clone (element) is considered "Not Validated". It is not feasible to remove the element from the printing step as this would involve further manipulations and a greater chance of tracking error. Thus, these non-validated elements are retained through the process but are categorized as "Not Validated" for the user.

6. How will the clone and spot location information be provided?

We will provide a list of the elements (clone name, Genbank accession number, putative identification) along with the spot location (block, column, row) with the arrays in an Excel spreadsheet that will be available to users via FTP download. This provides the user with the most information possible in the most generic and useable format, regardless of platform for analysis. There are numerous brands of scanners and these all require customized formats. It is the responsibility of each user to convert the data into a format useable by their own scanner and data analysis systems.

7. What kind of arrayer was used to print these arrays?

Intelligent Automation Systems (each machine is made slightly differently according to users requests; http://www.brooks.com/index.cfm).

8. What kind of pins were used to print the arrays, and in what orientation?

Telechem's Stealth Microspotting Pins 3 (Cat# SMP-3). They are arranged in a 12 x 4 pin fashion.

9. What is the distance between the pins?

4500 um between each pin which corresponds to the distance between each block, that is the distance between the top left spot in block one and the top left spot in block 2.

10. What should I do if I'm getting high background?

a). Make certain that your RNA is clean and not degraded (ie. 260/280 ratio between 1.8-2.1 and make certain RNA is not degraded by checking it on a gel).
b). Make certain that you have thoroughly cleaned your slide after incubation in pre-hybridization solution (see TIGR Potato Microarray Methods SOP 6.2.1 section 2b). If you see white streaks after washing the slides in water and isopropanol, repeat the washes until the slide is clear.

Last modified: Monday, 26-Jan-2009 14:33:18 EST