TIGR Potato cDNA Microarray Description

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TIGR Potato cDNA Microarray (10Kv4) Description

We have constructed several versions of our potato cDNA array. The current version is the "10K version 4". Previous versions include the "10K version 1, 2, 3" and the 5K version.

The elements on the microarray were selected from the potato stolon, root, microtuber, dormant tuber, germinating eye, healthy leaf, and Phytophthora infestans-challenged libraries (incompatible and compatible) sequenced at TIGR in collaboration with others on the NSF Potato Functional Genomics Project. Details on the sequencing of these can be found at http://www.tigr.org/potato/data/potato/est2.shtml.

A total of 15,264 cDNAs were selected for the microarray. This number includes clones selected for controls on the arrays (see below). The potato cDNA clones were rearrayed, resequenced (5' and 3') and the inserts were amplified using universal primers that flank the insertion site. All PCR products were run on agarose gels to check for amplification of single bands. Only 11,412 cDNA clones could be verified by both resequencing and agarose gel inspection. However, all 15,264 cDNAs were spotted in duplicate on the slides. Thus, there will be spots on the array that may hybridize to your RNA but could not be validated by our criteria. These clones are listed by 'Do not use. Not validated' in the name column and have a '0' in the ID column meaning they have NOT been validated. Please note that since all the clones are spotted in duplicate, there will be 22,824 useable elements (spots) but 32,448 total spots.

The clone list for the potato 10K version 4 cDNA array is available for download. This file provides information on the elements (clone name), spot location, Genbank number (both 5' and 3'), TIGR Plant Transcript Assembly (TA) ID, and putative identification (if available). Clones without a TA are listed as 'null' in the Plant Transcript Assembly column. Depending on the clustering results, the clone may be in two different TAs as the 5' and 3' sequences derived from the clone may not overlap. Also, not all sequences have a putative identification and their function remains unknown. A 'null' is used for clones without a putative identification. More detailed information on these clones can be found in the TIGR Plant Transcript Assemblies at http://plantta.tigr.org.

If you are using GenePix to quantitate your hybridizations, you can download the gal file for our 10K version 4 array at the TIGR Potato cDNA Microarray Layout page.

The control clones on the array include potato cDNA, potato genomic, tomato cDNA, and human spiking control clones. These represent genes involved in housekeeping functions, photosynthesis and defense responses. Not all of these clones are part of the potato gene index and thus do not have StGI numbers. Also, a majority of the potato genomic clones were made by PCR amplification of genomic DNA and sequence verification at TIGR. These have not been deposited in Genbank and thus do not have a Genbank accession number. There are also a few clones from the fungal pathogen, Phytophthora infestans, on the slide as controls for pathogen infection. A listing of the control clones can be found at TIGR Potato cDNA Microarray Control Clones page.

Protocols for using the TIGR Potato cDNA Microarray may be found at the TIGR Potato cDNA Microarray Protocols page. Note that we provide several labeling and hybridization methods, one for direct labeling and one for indirect labeling via amino allyl. We also provide methods for amplification of RNA. All of these methods work well on our potato slides and with Solanaceae RNA.

All cDNAs are printed on Corning Ultra Gaps Slides (#40015). For further information concerning the slide manufacturer:

    Corning/Costar Corporation
    P.O. Box 75122
    Charlotte, NC 2875-0909
    www.corning.com

Store slides in a dessicator prior to use in a light tight slide box.

 

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