Encoding growth factor identity in the temporal dynamics of FoxO3 under the combinatorial control of ERK and AKT Kinases

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.

本数据集仓库为Sampattavanich等学者2018年发表于《细胞系统》（Cell Systems）的论文《编码ERK与Akt协同调控下FoxO3的时间动态以识别生长因子身份》提供原始配套数据。

概述：叉头框O3转录因子（Forkhead box O3, FoxO3）是多种上游信号网络的整合节点，参与细胞周期阻滞、细胞凋亡、氧化应激、细胞迁移与细胞代谢等诸多生物学过程。包括磷酸化、能量应激、基因毒性应激及细胞因子在内的FoxO3调控因子，可调控其蛋白丰度、亚细胞定位与DNA结合能力。本研究旨在探究生长因子的种类与浓度如何被编码于FoxO3的激活动态过程中。此类转录因子往往会在12~24小时的周期内反复于激活与失活状态间切换。免疫印迹等技术会因细胞间的异步性而掩盖此类切换行为。与之相比，本研究通过荧光报告蛋白的延时显微成像技术发现，FoxO3展现出复杂的低波长与脉冲式转位动态，可响应ERK与Akt的协同调控，具备编码多种胞外生长因子种类与浓度的潜力。

数据集内容：本数据集包含可复现该论文所有图表的原始数据，文件格式为.MAT或.CSV。需将这些文件夹放置于Git仓库目录下的/rawdata文件夹中，以供读者自行复现全部图表。
/parentalVSreporter：该数据集用于复现图1B、补充图S1B与S1C。
/Workspace：该数据集对图1至图6中的所有功能主成分分析（functional principal component analysis, fPCA）与脉冲评分分析至关重要。
/dualsensors：该数据集用于复现图6B。
/western：该数据集用于复现图1C与补充图S1G。
/fixedcell：该数据集用于复现图7。
/Time-lapse video：该文件夹包含复现图1~2所用主数据集的视频文件，涵盖不同生长因子、不同给药剂量及不同药物预处理的实验样本。

若需进一步了解该数据集，请访问配套的HMS LINCS网站。