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PNAS Article Validates BioMark™ Digital Arrays for Profiling Transcription Factors from a Single Stem Cell

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Research published in the Proceedings of the National Academy of Science demonstrates that BioMark™ digital arrays, from Fluidigm Corporation, 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.
The digital array, on the other hand, is made to analyze single cell. 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.