Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 72

RICEATLAS
The RICEATLAS is a database housing rice transcriptome data covering various
types of tissues using laser capture microdissection (Jiao et al. 2009 ). It is housed
within the search engine of the Yale Virtual Centre for Cellular Expression Profiling
of Rice web address, and in the TIGR site.
Tilling Arrays
Tilling arrays are high-density oligonucleotide probes covering the genome in a
particular organism, and therefore are a platform for analysing expressed regions
throughout the genome. The method is effective in discovering novel genes and elu-
cidating their structure. For example, Seki and co-workers performed transcriptome
analysis in Arabidopsis under abiotic stress using whole-genome tilling array and
described a number of antisense transcripts induced by stress (Matsui et al. 2008 ).
At-TAX
Arabidopsis thaliana Tilling Array Express (At-TAX) is a whole-genome tilling
array resource for developmental expression analysis and transcript identification
(Laubinger et al. 2008 ; Zeller et al. 2009 ). The utility of tilling arrays has been ex-
tended recently by coupling this platform with an immunoprecipitation method (see
Sects. 3.6.13 and 3.6.14 below).
MADS
The MADS domain uses a chromatin immunoprecipitation (ChIP) method that has
been used to identify transcriptional regulator sites for somatic embryogenesis,
when coupled with the Affymetrix tilling array for Arabidopsis. This rather complex
method to use and master, nevertheless found approximately 2,000 sites of regula-
tion (Zheng et al. 2009 ).
ChIP-Seq
A methylcytosine immunoprecipitation (mCIP) method, in combination with Ara-
bidopsis tilling array, can map comprehensive DNA methylation sites; and is often
referred to as 'methylome' data (Zhang et al. 2006 ). Sequencing of co-precipitated
DNA and a protein using next generation sequencing, 'ChIP-seq', has also become
an important experimental approach (Park 2009 ). MACS and SOLiD ChIP-Seq
web sites contain information and commercial kits and alternative analysis using