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ARTICLE ABSTRACT
Nature Methods
Published online: 6 April 2009 | Corrected online: 19 April 2009 | doi:10.1038/nmeth.1315
mRNA-Seq whole-transcriptome analysis of a single cell
Fuchou Tang1,3, Catalin Barbacioru2,3, Yangzhou Wang2, Ellen Nordman2, Clarence Lee2, Nanlan Xu2, Xiaohui Wang2, John Bodeau2, Brian B Tuch2, Asim Siddiqui2, Kaiqin Lao2 & M Azim Surani1
Abstract
Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression profiling assay. Using our mRNA-Seq assay with only a single mouse blastomere, we detected the expression of 75% (5,270) more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads. Moreover, 8–19% of the genes with multiple known transcript isoforms expressed at least two isoforms in the same blastomere or oocyte, which unambiguously demonstrated the complexity of the transcript variants at whole-genome scale in individual cells. Finally, for Dicer1-/- and Ago2-/- (Eif2c2-/-) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common.
Nature Methods
Published online: 6 April 2009 | Corrected online: 19 April 2009 | doi:10.1038/nmeth.1315
mRNA-Seq whole-transcriptome analysis of a single cell
Fuchou Tang1,3, Catalin Barbacioru2,3, Yangzhou Wang2, Ellen Nordman2, Clarence Lee2, Nanlan Xu2, Xiaohui Wang2, John Bodeau2, Brian B Tuch2, Asim Siddiqui2, Kaiqin Lao2 & M Azim Surani1
Abstract
Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression profiling assay. Using our mRNA-Seq assay with only a single mouse blastomere, we detected the expression of 75% (5,270) more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads. Moreover, 8–19% of the genes with multiple known transcript isoforms expressed at least two isoforms in the same blastomere or oocyte, which unambiguously demonstrated the complexity of the transcript variants at whole-genome scale in individual cells. Finally, for Dicer1-/- and Ago2-/- (Eif2c2-/-) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common.