Encoding growth factor identity in the temporal dynamics of FoxO3 under combinatorial regulation by ERK and Akt

Published: 16 Apr 2018 | Version 1 | DOI: 10.17632/65fkdzt9x5.1
Contributor(s):

Description of this data

Sampattavanich et al., Cell Systems (2018)

This data repository provides raw datasets for accompanying the paper, "Encoding growth factor identity in the temporal dynamics of FoxO3 under combinatorial regulation by ERK and Akt" by Sampattavanich et al., Cell Systems (2018)

Synopsis:
Forkhead box O3 transcription factor (FoxO3) functions as an integrative node for diverse upstream signaling networks, and has been implicated in a number of biological processes including cycle arrest, apoptosis, oxidative stress, cell migration and cell metabolism. Regulators of FoxO3, including phosphorylation, energy stress, genotoxic stress, and cytokines, control its abundance, subcellular localization and DNA-binding capacity. In this paper we study how the identities and concentrations of growth factors are encoded in the dynamics of FoxO3 activation. Transcription factors like FoxO3 often switch between on and off states repeatedly over the course of a 12-24 hours period. Immunoblotting and similar methods can obscure this switching behavior due to asynchronicity between cells. In contrast, our use of time-lapse microscopy of fluorescent reporter proteins reveals that FoxO3 exhibits complex low wavelength and pulsatile translocation dynamics responsive to combinatorial control by ERK and Akt with the potential to encode the identities and concentrations of multiple extracellular growth factors.

Dataset Content:

This dataset includes raw datasets either in .MAT, or .CSV for regenerating all figures in the publication. These folders should be placed inside the /rawdata folder in the git repository folder so that the reader can generate these figures on their own.
/parentalVSreporter - This dataset is used to regenerate fig.1B, S1B and S1C.
/Workspace - This dataset is important for all fPCA and pulse score analysis in Fig.1-6
/dualsensors - This dataset is used to regenerate Fig.6B
/western - This dataset is used to regenerate Fig.1C and S1G
/fixedcell - This dataset is used to regenerate Fig.7
/Time-lapse video - This folder gives video files of the main dataset for Fig.1-2, varying different growth factors at various dosing, with different drug pre-treatment.

To learn more about this data, please also visit the accompanying HMS LINCS website shown below.

Experiment data files

Steps to reproduce

Accompanying matlab scripts can also be found in the provided github link. To reproduce plots in the paper:

  1. Clone the repo and install necessary toolbox
  2. Create a new directory called 'rawdata' at the top-most level of the git repo folder
  3. Download these files and place inside rawdata folder. Extract all zip files
  4. Visit our github repository for instruction to regenerate each specific figures

We also provide raw images and extracted data in LINCS-compatible CSV-format at HMS LINCS website.

Related links

peer reviewed

This data is associated with the following peer reviewed publication:

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases

Published in: Cell Systems

Latest version

Previous versions

  • Version 2

    2018-05-26

  • Version 1

    2018-04-16

    Published: 2018-04-16

    DOI: 10.17632/65fkdzt9x5.1

    Cite this dataset

    Sampattavanich, Somponnat; Steiert, Bernhard; Kramer, Bernhard; Gyori, Benjamin; Albeck, John; Sorger, Peter (2018), “Encoding growth factor identity in the temporal dynamics of FoxO3 under combinatorial regulation by ERK and Akt”, Mendeley Data, v1 http://dx.doi.org/10.17632/65fkdzt9x5.1

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Institutions

Mahidol University Faculty of Medicine Siriraj Hospital, Harvard Medical School

Categories

Systems Biology, Proteomics, Biological Sciences Quantitative Methods

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Licence

MIT Learn more

The files associated with this dataset are licensed under a MIT License licence.

What does this mean?

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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