The generation of genome-wide gene expression data for the reference plant Arabidopsis thaliana yielded important insights into transcriptional control of development, with genome-wide expression maps having become an indispensable tool for the research community. Specific gene expression profiles for various plant organs, developmental stages, growth conditions, treatments, mutants, or even single cell types are available (for example [1–7]). These data have helped to elucidate transcriptional networks and attending promoter motifs, to uncover gene functions, and to reveal molecular explanations for mutant phenotypes (for review ).
The most widely used platform for Arabidopsis is the Affymetrix ATH1 array [9, 10]. Its design used prior information in the form of experimentally confirmed transcripts and gene predictions, and was intended to provide information on most known transcripts. Although the ATH1 array includes more than 22,500 probe sets, it lacks almost one-third of the 32,041 genes found in the most recent TAIR7 annotation . All users of ATH1 arrays are confronted with a problem; as the number of newly discovered genes is rising, expression analysis becomes more and more restricted.
More unbiased detection of transcriptional activity can be achieved by sequencing techniques such as massively parallel signature sequencing and serial analysis of gene expression or, alternatively, by microarrays that interrogate the entire genomic sequence, so called 'whole genome tiling arrays' [12–14]. In contrast to arrays that are focused on gene expression, which contain only probes complementary to annotated genes, whole-genome tiling arrays are designed irrespectively of gene annotations and contain probes that are regularly spaced throughout the nonrepetitive portion of the genome . This includes intergenic and intronic regions, and whole-genome tiling arrays can therefore measure transcription from annotated genes, identify new splice and transcript variants of known genes, and even lead to the discovery of entirely new transcripts.
Outside the context of plants, tiling arrays have been used to detect transcriptional activity in the genome of several organisms, including baker's yeast, Caenorhabtidis elegans, Drosophila melanogaster, and humans [16–22]. Apart from the discovery of new transcripts, tiling arrays are useful for mapping the 5' and 3' ends of transcripts, and for the identification of introns (for example ). Perhaps most importantly, these studies have expanded our understanding of genome organization. Apparently, genomes give rise to many more transcripts than was previously assumed. Most of these are noncoding RNAs emerging from intergenic regions, a large portion of which had previously been underrated as 'junk' DNA . Although the functional relevance of the majority of these transcripts remains unclear, their abundance and the fact that they have escaped ab initio gene predictions highlight the advantages of whole-genome tiling arrays. Another group of transcripts that has frequently been ignored in the past are nonpolyadenylated transcripts. Up to 50% of distinct transcripts in human and C. elegans lack polyA tails; this phenomenon is neglected by most gene expression studies, which typically use polyA(+) RNA as starting material or oligo-dT-primers for reverse transcription [19, 20].
The first tiling array analyses of Arabidopsis and rice combined with sequencing of full-length cDNAs delivered important information about gene content, gene structure, and genome organization [14, 25–30]. Furthermore, gene expression profiling with tiling arrays of Arabidopsis mutants led to the identification of hundreds of noncoding transcripts that are normally silenced or removed by the exosome [31, 32].
In line with findings in yeast and animals, Yamada and colleagues  reported that many Arabidopsis genes are also transcribed in anti-sense orientation, implicating anti-sense transcription in gene regulation. More recent studies in yeast and mammals suggested that at least some of the signals may be due to artifacts of reverse transcription methods used to generate the probes for array hybridization [33, 34].
Here, we use the Affymetrix GeneChip® Tiling 1.0R Array (Affymetrix Inc., Santa Clara, CA, USA) to provide an initial whole-genome expression atlas for A. thaliana, dubbed 'Arabidopsis thaliana Tiling Array Express' (At-TAX), using RNA samples from 11 different tissues collected at various stages of plant development. We directly compare the performance of the tiling array, which contains one 25-base probe in each nonrepetitive 35 base pair (bp) window of the reference genome, with that of the 'gold standard' ATH1 array. We also report on the expression profile of over 9,000 annotated genes that are not represented on the ATH1 array. Applying a recently developed computational method for transcript identification to the tiling array data allowed us to identify regions not previously annotated as transcribed . Our data also suggest that most Arabidopsis transcripts expressed at detectable levels are polyadenylated. To benefit the Arabidopsis research community, we provide an online tool for visualization of gene expression estimates, along with a customized genome browser .