Supplementary data for "Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements"

S1 Appendix. Extended Methods and Materials.
https://doi.org/10.1371/journal.pcbi.1005174.s001
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S1 Table. Mean, standard deviation (sd), and coefficient of variation (cv) of the transcription intervals for the Plac/ara-1 promoter. The table shows the condition, number of exact intervals (samples), number of right-censored intervals (R-samples), and the estimated mean, sd, and cv of the intervals (considering exact and right-censored ones).
https://doi.org/10.1371/journal.pcbi.1005174.s002
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S2 Table. Presence or absence of on/off switching and number of identified steps in Plac/ara-1 promoter. The table shows the condition, the existence or absence (yes/no) of on/off switching, the durations of significant steps (Steps 1 to 3), the second-best fitting model (Alt model), and the difference in BICs (ΔBIC) of the second-best and the best fitting models and its lower bound.
https://doi.org/10.1371/journal.pcbi.1005174.s003
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S3 Table. Estimated model parameters for Plac/ara-1 promoter. The table shows the induction condition and the estimated parameter values. Here, , where T is the temperature in degrees Celsius.
https://doi.org/10.1371/journal.pcbi.1005174.s004
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S4 Table. Statistics of the on/off switching for Plac/ara-1 promoter. The table shows the condition, the fraction of time the gene is on (Duty cycle) and the average burst size and interval.
https://doi.org/10.1371/journal.pcbi.1005174.s005
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S5 Table. Mean, standard deviation (sd), and coefficient of variation (cv) of the transcription intervals for the PtetA promoter. The table shows the temperature condition, number of exact intervals (samples), number of right-censored intervals (R-samples), and the estimated mean, sd, and cv of the intervals.
https://doi.org/10.1371/journal.pcbi.1005174.s006
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S6 Table. Presence or absence of on/off switching and number of identified steps in the PtetA promoter. The table shows the temperature condition, the presence or absence of on/off switching (On/off), the durations of the significant steps (Steps 1 to 3), the second-best fitting model (Alt model), the difference in BICs (ΔBIC) of the second-best and the best fitting model, and its lower bound (LB).
https://doi.org/10.1371/journal.pcbi.1005174.s007
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S7 Table. List of promoters and measurement conditions used in the manuscript. The table shows an arbitrary condition ID, the promoter, concentrations of the inducers (IPTG (mM), Ara (L-arabinose; %), and aTc (anhydrotetracycline; ng/mL)), and the temperature (°C).
https://doi.org/10.1371/journal.pcbi.1005174.s008
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S8 Table. List of all intervals between the production of consecutive transcripts used in the manuscript. The table shows an arbitrary interval ID, condition ID (a foreign key to), the lower (Interval LB) and upper bounds (Interval UB), and the ID of the interval that precedes in time (Previous Interval ID) for each interval observed in the cells under both promoters in each condition. The order of the rows has no particular meaning.
https://doi.org/10.1371/journal.pcbi.1005174.s009
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S1 Fig. Mean and standard deviation of transcription intervals generated using a Monte Carlo simulation as a function of temperature for the Plac/ara-1 promoter. The dashed curves represent the means and standard deviations of the best fitting models.
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S2 Fig. Mean and standard deviation (sd) of transcription intervals as a function of the relative change in , , and .
The horizontal axis corresponds to the relative value in the specified parameter. The dashed curves are the asymptotes discussed in the text. The pivot parameters result in a mean of 2 and sd of .
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S3 Fig. Lower bound for the coefficient of variation of transcription intervals as a function of the relative durations between pre- and post-commit stages. Blue points represent instances of random models. Green curves are the cv lower bounds for different number of steps n in the post-commit stage: from top to bottom: 1, 2 (solid curve; the model in Eq (1)), 3, 4, and 5. The dotted black line is the absolute lower bound attained with a constant-duration post-commit stage (n = ∞).
https://doi.org/10.1371/journal.pcbi.1005174.s012
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S4 Fig. Mean, standard deviation (sd), and coefficient of variation (cv) of the transcription intervals for the Plac/ara-1 promoter under full induction, and the corresponding best fitting model. The data points correspond to those shown in S1 Table. Error bars denote one sd of the estimator uncertainty.
https://doi.org/10.1371/journal.pcbi.1005174.s013
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S5 Fig. Mean, standard deviation (sd), and coefficient of variation (cv) of the transcription intervals for the PtetA promoter under full induction, and the corresponding best fitting model. The data points correspond to those shown in S5 Table. Error bars denote one sd of the estimator uncertainty.
https://doi.org/10.1371/journal.pcbi.1005174.s014
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S6 Fig. Mean, standard deviation (sd), and coefficient of variation (cv) of the transcription intervals when varying each parameter independently around the parameter values found for the PtetA promoter, full induction.
The numeric labels for the crosses indicate temperature (°C). The data points are derived from the best fitting model.
https://doi.org/10.1371/journal.pcbi.1005174.s015
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