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J. Jacak, H. Schnidar, L. Muresan, G. Regl, A. Frischauf, F. Aberger, G. Schütz, J. Hesse:
"Expression analysis of multiple myeloma CD138 negative progenitor cells using single molecule microarray readout";
Journal of Biotechnology, 164 (2013), 525 - 530.

We present a highly sensitive bioanalytical microarray assay that enables the analysis of small genomic
sample material. By combining an optimized cDNA purification step with single molecule cDNA detection
on the microarray, the platform has improved sensitivity compared to conventional systems, allowing
amplification-free determination of expression profiles with as little as 600 ng total RNA. Total RNA from
cells was reverse transcribed into fluorescently labeled cDNA and purified employing a precipitation
method that minimizes loss of cDNA material. The microarray was scanned on a fluorescence chipreader
with single molecule sensitivity. Using the newly developed platform we were able to analyze
the RNA expression profile of a subpopulation of rare multiple myeloma CD138 negative progenitor (MM
CD138neg) cells. The high-sensitivity microarray approach led to the identification of a set of 20 genes differentially
expressed in MM CD138neg cells. Our work demonstrates the applicability of a straight-forward
single-molecule DNA array technology to current topics of molecular and cellular cancer research, which
are otherwise difficult to address due to the limited amount of sample material.

Expression profiling Microarray Subpopulation analysis Single molecule detection Fluorescence microscopy