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. Author manuscript; available in PMC: 2018 Dec 28.
Published in final edited form as: Methods Mol Biol. 2013;1042:47–60. doi: 10.1007/978-1-62703-526-2_4

Figure 3.

Figure 3.

Fluctuation analysis of transcription activity. A) Representative individual fluorescence image from a single transcription site time series. Scale bar = 1.5 μm. B) Surface plot of panel A. C) Two-dimensional Gaussian fit to the data in panel A. D) Transcription site intensity trajectory. Each data point in the curve comes from a determination of spot intensity using the Gaussian mask algorithm. The spot is tracked over many frames, and missing frames are interpolated based on the last known position of the spot. The final output of the tracking program is the fluorescence of the transcription site as a function of time. E) Autocorrelation. The time series intensity trajectory is autocorrelated using a multi-tau correlation algorithm. The x-axis is the correlation decay; the y-axis is the amplitude of the autocorrelation. The fit parameters for the 5’ UTR case are shown graphically: the amplitude of the autocorrelation is related to the number of polymerases (cT), and the characteristic decay is related to the dwell time of the polymerase (T).