Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays

  • A Corrigendum to this article was published on 01 October 2000


We describe a novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 μm diameter microbeads. After constructing a microbead library of DNA templates by in vitro cloning, we assembled a planar array of a million template-containing microbeads in a flow cell at a density greater than 3 × 106 microbeads/cm2. Sequences of the free ends of the cloned templates on each microbead were then simultaneously analyzed using a fluorescence-based signature sequencing method that does not require DNA fragment separation. Signature sequences of 16–20 bases were obtained by repeated cycles of enzymatic cleavage with a type IIs restriction endonuclease, adaptor ligation, and sequence interrogation by encoded hybridization probes. The approach was validated by sequencing over 269,000 signatures from two cDNA libraries constructed from a fully sequenced strain of Saccharomyces cerevisiae, and by measuring gene expression levels in the human cell line THP-1. The approach provides an unprecedented depth of analysis permitting application of powerful statistical techniques for discovery of functional relationships among genes, whether known or unknown beforehand, or whether expressed at high or very low levels.

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Figure 1: Ligation-based sequence determination using the type IIs restriction endonuclease BbvI.
Figure 2: Use of encoded adaptors to identify four bases in each ligation–cleavage cycle.
Figure 3: Flow cell design and use.
Figure 4: MPSS system.
Figure 5: A false-color image of a portion of a microbead array with inset showing raw signature data from the microbead at the indicated position.
Figure 6: Comparison of MPSS analysis with expressed sequence tag (EST) sequencing.


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The authors thank Steve Macevicz of Lynx Therapeutics for preparing the manuscript; Mel Kronick of Agilent Technologies and Dan Pinkel of the Cancer Center, Department of Laboratory Medicine, University of California, San Francisco, for helpful comments; and Larry DeDionisio and Victor Quijano of Lynx Therapeutics for technical assistance.

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Correspondence to Sydney Brenner.

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Brenner, S., Johnson, M., Bridgham, J. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18, 630–634 (2000).

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