Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 68

High Density Mapping of TSS
The method has been applied to perform high-density mapping of TSS in Arabidop-
sis, and identify genome-scale presence of plant promoters (Yamamoto et al. 2009 ).
The data set of Arabidopsis CT-MPSS tags is accessible from the PPDB site, a plant
promoter database that provides promoter information and motifs for Arabidopsis
and rice (Yamamoto and Obokata 2008 ).
Hybridisation-BasedPlatforms
DNA microarrays had their beginning with Brown's research at Stanford University
in 1995 (Schena et al. 1995 ), and since then, microarray and DNA chip-related tech-
nologies have advanced rapidly; and their application has expanded to a wide vari-
ety of life science disciplines. DNA microarray or GeneChip analysis are designed
to acquire comprehensive data of the molecular abundance of each molecule in a
given sample, based on its simultaneous hybridization with a large population of
synthetic (DNA or cDNA) oligonucleotide species; usually immobilized on a glass
slide or on a silicon chip. With the recent and rapid increase in the number of se-
quenced plant species, the availability of DNA microarrays have also increased for
transcriptome analysis. For example, Seki and co-workers designed a custom DNA
microarray that uses 7,000 full-length cDNA clones of Arabidopsis as probes, and
then successfully screened genes in response to abiotic stresses using a two-colour
method (Seki et al. 2002a ). With the recent increase in commercially available DNA
microarrays, laboratories are able to use a particular DNA microarray design to
obtain transcriptome data from many experiments, and in so doing accumulate com-
prehensive information on organism-specific transcriptional data. Gene expression
analysis and gene chip technology, URL web sites and the use of such technology
are detailed in Table 2.5 .
DNA Microarray Types
DNA microarrays can be classified into two types: (i) the 'spotting' type, which
was developed at Stanford University; and (ii) the 'on-chip synthesis' type based on
manufactured probes by a number of molecular biology companies. The spotting
type was commonly used during the early years of transcriptome research. This
method entailed preparing DNA microarrays by spotting a cDNA solution onto a
glass slide, but spot microarrays are being replaced quickly by on-chip synthesis
type.