Pan-genome isolation of low abundance transcripts using SAGE tag.

The (serial analysis of gene expression) method is sensitive at detecting the lower abundance transcripts. More than a third of human duanyu1798 tags identified are novel representing the low abundance unknown transcripts. Using the GLGI method (generation of longer 3' EST from duanyu1798 tag for gene identification), we converted 1009 low-copy, human X chromosome-specific duanyu1798 tags into 10210 3' ESTs. We identified 3418 unique 3' ESTs, 46% of which are novel and originated from the lower abundance transcripts. However, nearly all 3' ESTs were mapped to various regions across the genome but not X chromosome. Detailed analysis indicates that those 3' ESTs were isolated by duanyu1798 tag mis-priming to the non-parent transcripts. Replacing duanyu1798 tags with non-transcribed genomic DNA tags resulted in poor amplification, indicating that the sequence similarity between different transcripts contributed to the amplification. Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through duanyu1798 tags mis-priming.

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