SPATIOTEMPORAL COORDINATION OF TRANSCRIPTION PREINITIATION COMPLEX ASSEMBLY IN LIVE CELLS. Nguyen et. al.

Published: 10 August 2021| Version 1 | DOI: 10.17632/3xktk72wbd.1
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Description

Live-cell, single-molecule tracking (SMT) data of transcription preinitiation complex (PIC) components in Saccharomyces cerevisiae

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Steps to reproduce

For each PIC component, fast- and slow-tracking data are organized within folders titled according to the genetic background (AA, Anchor-Away). Individual replicate datasets (REP1... REP3) are included when applicable. Note that these data are localization and tracking output from DiaTrack and contain only nuclear tracks. Please reach out to the Lead Contact (Carl Wu, wuc@jhu.edu) for raw movies. To process these data, 1. Obtain the Sojourner package at https://github.com/sheng-liu/sojourner, 2. Find basic scripts to run with Sojourner in R-Studio in the SCRIPTS folder, 3. To analyze fast-tracking data using Spot-On (https://spoton.berkeley.edu), import each .csv file as "MOSAIC suite" format with 10 ms framerate and 107 nm/pix. For most dataset, we use the following parameters for kinetic modeling: Bin width: 0.01-0.02 µm, Number of timepoints: 5; Jumps to consider: 5, Max jump=0.8-1.2 µm; Localization error: Fit it from data, dZ=0.58 µm; Model Fit: CDF, Iterations: 3. If fitted localization error is too small (<0.02 µm), rerun fit with error set to 0.035 µm.