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Nature Methods 6, 377–382 (1 May 2009) | doi:10.1038/nmeth.1315

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang , Catalin Barbacioru , Yangzhou Wang , Ellen Nordman , Clarence Lee , Nanlan Xu , Xiaohui Wang , John Bodeau , Brian B Tuch , Asim Siddiqui , Kaiqin Lao & M Azim Surani

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|[minus]|/|[minus]| and Ago2|[minus]|/|[minus]| (Eif2c2|[minus]|/|[minus]|) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common.