RNA Detection

(‘.log’), and a scatter plot that indicates which spots have been

identified as transcripts and which have been identified as foci,

based on their intensity and size (‘_ScatterPlot_*.png’). These

files provide more background information on the results and

the analysis.

Acknowledgments

This work was supported by MPI-CBG core funding, a Human

Frontier Science Program Career Development Award [CDA-

00060/2012-C] to NLV; and a Boehringer Ingelheim Fonds

PhD fellowship to LCS. We thank Pavel Vopalensky for critically

reading the manuscript, Julia Eichhorn for taking photos of the

sectioning procedure, and Jan Philipp Junker and Alexander van

Oudenaarden for initial advice on smFISH.

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