Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
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Author
Zhang, Kun
Li, Jin Billy
Gao, Yuan
Egli, Dieter
Xie, Bin
Deng, Jie
Li, Zhe
Lee, Je-Hyuk
Leproust, Emily M
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https://doi.org/10.1038/nmeth.1357Metadata
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Zhang, Kun, Jin Billy Li, Yuan Gao, Dieter Egli, Bin Xie, Jie Deng, Zhe Li, et al. 2009. “Digital RNA Allelotyping Reveals Tissue-Specific and Allele-Specific Gene Expression in Human.” Nat Meth 6 (8) (July 20): 613–618. doi:10.1038/nmeth.1357.Abstract
We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock captured SNPs from the transcriptome. We characterized four cell lines established from two human subjects in the Personal Genome Project. Approximately 11–22% of the heterozygous mRNA-associated SNPs show allele-specific expression in each cell line; and 4.3–8.5% are tissue-specific, suggesting the presence of tissue-specific cis-regulation. When applied to two pairs of sibling human embryonic stem cell lines, the sibling lines were more similar in allele-specific expression than were the genetically unrelated lines. We found that the variation of allelic ratios in gene expression among different cell lines is primarily explained by genetic variations, much more so than by specific tissue types or culturing conditions. Comparison of expressed SNPs on the sense and anti-sense transcripts suggested that allelic ratios are primarily determined by cis-regulatory mechanisms on the sense transcripts.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742772/Terms of Use
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http://nrs.harvard.edu/urn-3:HUL.InstRepos:25757165
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