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PNAS Article Validates BioMark(TM) Digital Arrays for Profiling Transcription Factors From a Single Stem Cell

Posted on: Tuesday, 21 November 2006, 15:01 CST

Research published in the November 21, 2006 issue of the Proceedings of the National Academy of Science (PNAS) demonstrates that BioMark™ digital arrays, in conjunction with PCR, provide a new tool for the study of gene regulatory networks. In the study, digital arrays were used to quantify genes on an absolute copies-per-cell basis, within five classes of hematopoietic stem cell precursors taken from mouse bone marrow.

Results showed there are divergent patterns of gene expression within classes of common myeloid progenitors and significant differences in the housekeeping transcript GAPDH. This divergence underscores the need to measure transcripts from single cells, in order to clearly understand cell programming.

"We believe that digital array technology will have significant impact on the pace of stem cell research," said Dr. Irving Weissman, an author of the report and the Virginia & D.K. Ludwig Professor for Clinical Investigation in Cancer Research at Stanford School of Medicine and director of the Institute for Stem Cell Biology and Regenerative Medicine.

Digital arrays have the potential to overcome difficulties inherent to PCR assays implemented on microplate platforms. Traditional mRNA assays involve aggregate measurements on large numbers of cells, which can mask the key regulatory states which determine cell fate. Single-cell protocols are available, but they tend to be overly complex and rely on conventional, macro-volume PCR.

The digital array, on the other hand, is well suited to single cell analysis. It works by partitioning a mixture of sample and assay components into approximately 1,000 nano-volume reaction chambers. The architecture of the chip, as well as the loading of an appropriately dilute sample, ensures every chamber contains either 1 copy or no copy of the target gene (cDNA). After on-chip thermal cycling, only the chambers that are positive for the gene give a fluorescent signal, which allows the copy number for a particular cell to be accurately counted -- a digital PCR.

Authors of the research article include Luigi Warren, of the California Institute of Technology, Pasadena, CA; David Bryder, of Lund University, Lund, Sweden; Irving Weissman of Stanford University, Stanford, CA; and Professor Stephen Quake, a Howard Hughes Medical Institute Investigator, of Stanford University, Stanford, CA.

About Fluidigm

Fluidigm Corporation develops and distributes systems based on the unique properties of integrated fluidic circuits (IFCs) to precisely control fluids on a nanovolume scale. The company's vision is to create and to lead a new industry in which IFCs bring unparalleled efficiencies to the life science and allied fields. Based in South San Francisco, California, the Company is privately held and backed by premier investors: Versant Ventures, Euclid SR Partners, InterWest Partners, Alloy Ventures, Lehman Brothers Healthcare Fund, the Singapore EDB, Bruce Burrows, Lilly BioVentures, the Invus Group, SightLine Partners, AllianceBernstein and GE Equity.

Source: Business Wire

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