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RNA-seq on Illumina GA system might be problematic, and this PolyA-seq approach seems to be better. As authors mentioned, it is likely to be more sensitive than Affymetrix GeneChip data, while GeneChip still has advantages in cost, automation and data handling though. You can download SSA files of these two data sets. GSE30198.ssa (PolyA-seq) www.sugarsync.com GSE2361.ssa (GeneChip) www.sugarsync.com Data Source: www.ncbi.nlm.nih.gov Summary: We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat. www.ncbi.nlm.nih.gov Summary: We performed expression profiling of 36 types of normal human tissues and identified 2503 tissue-specific genes. We then systematically studied the expression of these genes incancers by re-analyzing a large collection of published DNA microarray datasets. Our study shows that integration of each gene's breadth of expression (BOE) in normal tissues is important for biological interpretation of the expression profiles of cancers in terms of tumor differentiation, cell lineage and metastasis. Twenty five total RNA specimens were purchased from Clontech (Palo Alto, CA), Ambion (Austin, TX) and Strategene (La Jolla, CA). We tried to...
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