Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy
Jae Bum Kim,1,2*
Gregory J. Porreca,2*
Lei Song,2
Steven C. Greenway,2
Joshua M. Gorham,2
George M. Church,2
Christine E. Seidman,1,2,3
J. G. Seidman2
We describe a sensitive mRNA profiling technology, PMAGE (for "polony multiplex analysis of gene expression"), which detects messenger RNAs (mRNAs) as rare as one transcript per three cells. PMAGE incorporates an improved ligation-based method to sequence 14-nucleotide tags derived from individual mRNA molecules. One sequence tag from each mRNA molecule is amplified onto a separate 1-micrometer bead, denoted as a polymerase colony or polony, and about 5 million polonies are arrayed in a flow cell for parallel sequencing. Using PMAGE, we identified early transcriptional changes that preceded pathological manifestations of hypertrophic cardiomyopathy in mice carrying a disease-causing mutation. PMAGE provided a comprehensive profile of cardiac mRNAs, including low-abundance mRNAs encoding signaling molecules and transcription factors that are likely to participate in disease pathogenesis.
1 Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.
2 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
3 Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: seidman{at}genetics.med.harvard.edu (J.G.S.); cseidman{at}genetics.med.harvard.edu (C.E.S.)
