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PLoS One. 2012;7(2):e30794. doi: 10.1371/journal.pone.0030794. Epub 2012 Feb 8.

Highly parallel genome-wide expression analysis of single mammalian cells.

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  • 1Research and Development, Illumina, Inc, San Diego, California, United States of America.

Erratum in

  • PLoS One. 2012;7(2). doi: 10.1371/annotation/3f0ddf41-2e7a-4b56-93c2-2731f2890b19. Loring, Jeanne F [added].



We have developed a high-throughput amplification method for generating robust gene expression profiles using single cell or low RNA inputs.


The method uses tagged priming and template-switching, resulting in the incorporation of universal PCR priming sites at both ends of the synthesized cDNA for global PCR amplification. Coupled with a whole-genome gene expression microarray platform, we routinely obtain expression correlation values of R(2)~0.76-0.80 between individual cells and R(2)~0.69 between 50 pg total RNA replicates. Expression profiles generated from single cells or 50 pg total RNA correlate well with that generated with higher input (1 ng total RNA) (R(2)~0.80). Also, the assay is sufficiently sensitive to detect, in a single cell, approximately 63% of the number of genes detected with 1 ng input, with approximately 97% of the genes detected in the single-cell input also detected in the higher input.


In summary, our method facilitates whole-genome gene expression profiling in contexts where starting material is extremely limiting, particularly in areas such as the study of progenitor cells in early development and tumor stem cell biology.

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