Pine Microarray (Release 1) Description

The elements on the microarray were selected from the pine embryo-derived cDNA libraries sequenced at TIGR in collaboration with Dr. John Cairney as part of the NSF Genomics of Loblolly Pine Embryogenesis Project. Details on the sequencing and the origins of the cDNA libraries of these clones can be found at: http://www.tigr.org/tdb/e2k1/pine/pine_status.shtml.

A total of 16,992 cDNAs were selected for the microarray. The pine cDNA clones were rearrayed, resequenced, 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 12,536 clones could be verified by both resequencing and agarose gel inspection. However, all 16,992 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 in the "can_use" column with a value of "0" whereas the validated clones have a can_use value of "1".

We have provided you with a list of the elements, clone name, Genbank number, TIGR Pine Gene Index TC number (if available), and putative identification (if available). Most clones are members of a TC and will have a TC number. Clones without a TC are listed as null in the Pine Gene Index TC column. 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 DFCI Pine Gene Index.

Methods used successfully at TIGR with pine microarrays can be found at http://www.tigr.org/tdb/e2k1/pine/pine_protocols.shtml.

The microarray platform has been deposited into GEO and has been assigned the accession GPL5189.

A Gene Array List that contains a list of elements with clone name, TIGR pine gene index TC number, Genbank number, putative identification AND and spot location is available for download (Last updated Nov 8, 2005) (gal, 3.1M).

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.

When the barcode is at the bottom and facing up-the DNA side of the slide is facing you. Hybridize on this side (the one with the barcode).

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	Barcode

An actual hybridization with the blocks labeled is shown below.

If you have any questions on this release of the TIGR Pine Microarrays, please contact us at pine@tigr.org.

The NSF Genomics of Loblolly Pine Embryogenesis Project at IPST and TIGR is funded by the National Science Foundation.