Work Packages

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The work plan is organized in 6 Work Packages (see figure below). Overall, WPs 1 to 3 aim to develop all the required molecular tools (WP1), and hardware and software (WP3) to acquire an high-throughput data set of DNA, mRNA and protein images in single cells in time and space (WP2). WP4 is transversal and dedicated to data management, integration and modelling. WP5 will aim to disseminate and exploit project´s results, while WP6 will ensure professional management of the project and the consortium.

 

                                 

 

WP1: Targeting strategies for live cell imaging (WP leader: CRG)

We will develop one targeting strategy against the FP fused with the coding gene, to image genes at the DNA, mRNA and protein level. We have two sub-objectives:

1) Develop one targeting strategy to knock in the FP to tag gene loci and use it as bait to image DNA, mRNA and protein of any specific gene

2) Develop efficient probes to target the DNA of a gene locus and the correspondent mRNA and protein products.

 

WP2: Live cell super resolution imaging of mESCs upon perturbation (WP leader: HUJI)

We will use two already generated tagged mESC clones (Rex-GFP and -catenin-GFP) to achieve imaging of one gene locus and its products. We plan to:

1) Visualize the DNA of gene loci and the corresponding mRNAs and protein products in living cells at nanoscale resolution and in time;

2) Identify the changes of the DNA structure during the process of differentiation as compared to the stem cell state

3) Visualize and quantify mRNA production, movement and spatial distribution as well as to study protein localization, kinetics and distribution in single cells during differentiation

 

WP3: Development of super-resolution CellViewer (WP leader: ICFO)

We will develope CellViewer techonologies to image DNA, mRNA and protein dynamics and spatial organization with high-throughput and high spatiotemporal resolution. We include three sub-objectives:

1) Automate and miniaturize the optomechanical components required for SR microscopy

2) Develop smart data acquisition software that will enable unsupervised imaging sessions with SR microscopy

3) Use the CellViewer to analyse the function of several genes important in mESC differentiation after Wnt and RA-perturbation

 

WP4: Data management, integration and modelling (WP leader: CRG)

In this work package we will cover data management and public dissemination; statistical analysis, data exploration and visualisation; data integration, systems biology mathematical model building and fitting. It cooperates with WPs 1-3 on data quality and data production, managing potential sources of bias and noise or other limitations, and on biological data interpretation. Developed data analysis workflows that are associated with publications will be produced as executable documents, i.e. as fully third-party reproducible software documents that include textual explanation and all software inputs (data, parameters) and outputs (figure, tables, parameter estimates, hypothesis tests)

 

WP5: Dissemination and Exploitation (WP leader: CRG)

This workpackage plan comprises 3 different objectives:

1) Dissemination of results to the research community and relevant stakeholders from the public and private sector
2) Exploitation of results for further research, and commercialization
3) Communication of project activities to main stakeholders (researchers, technology sector, general public)

 

WP6: Coordination and Management (WP leader: CRG)

The coordination and management aims to address the following goals:

1) Coordination of research and innovation activities
2) Effective project and consortium management to achieve planned objectives within the assigned time frame and budget, and at the highest quality
3) Management of internal and external communication activities, and other horizontal aspects, as gender equality