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Science 6 August 2004:
Vol. 305. no. 5685, p. 846
DOI: 10.1126/science.1099247
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Multiplex Detection of RNA Expression in Drosophila Embryos

Dave Kosman,1 Claudia M. Mizutani,1 Derek Lemons,1 W. Gregory Cox,2 William McGinnis,1 Ethan Bier1*

We present a fluorescence-based, multiplex in situ hybridization method that permits the simultaneous detection of five differently labeled antisense RNA probes and up to seven different transcripts in a single Drosophila embryo. We also show that it should be possible to increase the number of detected transcripts substantially with nascent transcript multiplex fluorescent in situ hybridization. These multiplex methods fill a current technological gap between high-resolution in situ hybridization with one or two fluorescently labeled probes and low-resolution but genome-wide microarray RNA profiling and should be of great utility in establishing gene networks.

1 Section of Cell and Developmental Biology, University of California–San Diego, La Jolla, CA 92093, USA.
2 Molecular Probes, Inc., 29851 Willow Creek Road, Eugene, OR 97402, USA.

* To whom correspondence should be addressed. E-mail: ebier{at}ucsd.edu

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