The Affymetrix Whole Genome Array

Town, Christopher ChrisD. cdtown at
Fri May 3 17:33:51 EST 2002

>TIGR and Affymetrix are pleased to report the recent completion of the
Arabidopsis whole genome Affymetrix GeneChip* that has been developed as
part of the TIGR reannotation effort (see also
t=-6&item_id=278919). The design takes advantage of recent developments in
the Affymetrix GeneChip* technology that incorporate reductions in both
feature size and the number of probe pairs per gene. This allowed us to
place ~22,700 probe sets on the new array. To best represent the >26,000
annotated genes, precedence was given to genes for which either expression
evidence or a credible database match exist. Among the remaining
"hypothetical" genes, we nominated every singleton and at least one member
of each paralogous family. We also chose to represent very closely related
gene pairs by a single probe set, thus allowing us to incorporate an
additional ~1,000 genes. Altogether, the new ATH1 array represents ~24,000
genes. A list of these genes can be found at the TIGR ftp site
Affymetrix will make the array available to the research community in two
phases. At this time, and until full QC is completed, Affymetrix is
accepting orders only for whole Made to Order lots (80-90 probe arrays)
which will be ready in mid-May. Following full QC, the arrays will become
available as a commercial, fully supported Affymetrix product (packs of 5
and 30 probe arrays) in late summer.

Chris Town
Visiting Investigator
The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD 20850.

Office phone: 301-838-3523
To page me at TIGR: 301-838-0200
Fax: 301-838-0208

Home phone: 301-990-0878



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