Our analysis of gene imprinting was restricted to those genes associated with methylation differences, but other epigenetic mechanisms, such as silencing mediated by Polycomb group complexes, are also important for maintaining imprinted expression. Relatively few large-scale unbiased screens of allelic expression patterns have been performed in plants. Allele-specific expression analysis in endosperm of reciprocal hybrids of maize indicates that most genes are expressed according to the contribution of the parental genomes, although a small proportion of the genes studied exhibited parent-of-origin specific expression patterns. The advent of high throughput RNA sequencing technologies makes it possible to more directly assess the relative quantities of steady-state transcripts derived from maternally or paternallyinherited alleles. Similar approaches have successfully identified genes imprinted during different stages of mouse development. Here we assay imprinted gene expression by performing high throughput sequencing on poly-A selected RNA from embryo and endosperm derived from reciprocal crosses AbMole Metaproterenol Sulfate between two Arabidopsis thaliana accessions, Ler and Col-0. This strategy AbMole 4-Chloropropiophenone allowed us to distinguish transcripts derived from the maternally inherited or paternally inherited allele for a portion of expressed genes with Ler/Col-0 single nucleotide polymorphisms. We identified.200 genes with parentally biased expression patterns. Our experimental strategy is particularly robust for identifying paternally expressed imprinted genes, as transcripts derived from the paternal genome must come from one of the fertilization products. Over 40 genes are predominantly paternally expressed, including a large number of transcription factors and chromatin related proteins. Most of the imprinted genes we identify exhibit parentally biased expression rather than complete monoallelic expression, suggesting that dosage regulation is an important factor in gene imprinting. Approximately 10,300 genes from each tissue had at least 15 informative reads when data from reciprocal crosses were combined. These genes exhibited a range of maternal to paternal expression ratios, but the average percent maternal transcripts for each gene in the embryo and endosperm was near the expectation of 50% and 67%, respectively, based on the genomic DNA content of each tissue. This is consistent with studies of maize endosperm, which show that expression is proportional to the genomic contribution of the parents for most genes. To identify imprinted genes we used the Storer-Kim method to test whether the proportion of maternal and paternal reads for each gene was significantly different from expectations, taking into account the allelespecific read counts from both reciprocal crosses in order to distinguish parent-of-origin effects from strain-specific effects. We initially considered genes with a p-value less than 0.01, identifying 148 potential imprinted genes in the embryo and 1437 in the endosperm.