Abstract
This protocol provides a step-by-step approach to perturb single cells with time-varying stimulation profiles, collect distinct signaling responses, and use these to infer a system of ordinary differential equations to capture and predict dynamics of protein-protein regulation in signal transduction pathways. The models are validated by predicting the signaling activation upon new cell stimulation conditions. In comparison to using standard step-like stimulations, application of diverse time-varying cell stimulations results in better inference of model parameters and substantially improves model predictions. For complete details on the use and results of this protocol, please refer to Jashnsaz et al. (2020).
| Original language | English |
|---|---|
| Article number | 100660 |
| Journal | STAR Protocols |
| Volume | 2 |
| Issue number | 3 |
| DOIs | |
| State | Published - Sep 17 2021 |
Funding
G.N. is supported by NIH, United States, DP2 GM11484901, NIH R01GM115892, NIH R01GM140240, Vanderbilt Deans Faculty Fellow award, and Vanderbilt Startup Funds. Z.R.F. and B.M. are supported by NIH, United States, R35 GM124747. Z.R.F. was also supported by the Agence Nationale de la Recherche, France, and by ANR-18-CE91-0002, CyberCircuits. Z.R.F. is currently with the Center for Nonlinear Studies at Los Alamos National Laboratory. The authors thank Jason Hughes, Alexander Thiemicke, Benjamin Kesler, Rama Ali, and Blythe Hospelhorn for the discussion. This study used resources at the Advanced Computing Center for Research and Education (ACCRE) at Vanderbilt University, Nashville, TN (NIH, United States, S10 Shared Instrumentation Grant 1S10OD023680-01 [Meiler]). Conceptualization, G.N. B.M. H.J. and Z.R.F.; methodology, G.N. B.M. H.J. and Z.R.F.; software, G.N. B.M. H.J. and Z.R.F.; validation, H.J. and Z.R.F.; formal analysis, H.J.; investigation, H.J.; data curation, H.J.; writing \u2013 original draft, H.J.; writing \u2013 review & editing, H.J. G.N. B.M. and Z.R.F.; visualization, H.J.; supervision, G.N. and B.M. project administration, G.N. and H.J.; funding acquisition, G.N. and B.M. The authors declare no competing interests. G.N. is supported by NIH , United States, DP2 GM11484901 , NIH R01GM115892 , NIH R01GM140240 , Vanderbilt Deans Faculty Fellow award, and Vanderbilt Startup Funds . Z.R.F. and B.M. are supported by NIH , United States, R35 GM124747 . Z.R.F. was also supported by the Agence Nationale de la Recherche , France, and by ANR-18-CE91-0002 , CyberCircuits. Z.R.F. is currently with the Center for Nonlinear Studies at Los Alamos National Laboratory. The authors thank Jason Hughes, Alexander Thiemicke, Benjamin Kesler, Rama Ali, and Blythe Hospelhorn for the discussion. This study used resources at the Advanced Computing Center for Research and Education (ACCRE) at Vanderbilt University, Nashville, TN ( NIH , United States, S10 Shared Instrumentation Grant 1S10OD023680-01 [Meiler]).
Keywords
- Cell Biology
- Cell-based Assays
- Computer sciences
- Microscopy
- Model Organisms
- Signal Transduction
- Single Cell
- Systems biology