Data Management, Processing and Analysis

Data Management, Processing and Analysis

In the life cycle of a biological data, which goes from its acquisition to the formatting of results, the processing and analysis constitute a key step to making sens of the data. Analysis uses a set of mathematical and statistical operations whose goal is to improve the quality of the data and to extract relevant information.

Whether the data is acquired on or off site, the data management and analysis platform offers a set of skills and makes available to users computing and software resources covering the fields of processing, analysis, instrumental development and mathematics/statistics. It is therefore possible to propose targeted offers ranging from the reconstruction of raw data to their exploitation. Depending on the user’s request, dedicated staff will evaluate the needs and propose an adapted service ranging from support to autonomy.

EXPERTISE

EQUIPEMENTS

The platform relies on a set of analysis stations with sufficient computing power and high-performance graphics cards for the analysis of large volumes of data, the modeling and the visualization of very high-resolution 3D & 4D images using the most powerful software available at the moment.

3  Imaris (Bitplane) licences

  • 3D & 4D modeling, 2D & 3D tracking

2 Amira (ThermoFisher) licences 

  • 3D modeling, 3D & 4D image processing

1 Vision 4D (Arivis) licence

  • 3D & 4D modeling, pixel & object classification
iLastik Machine Learning

CONTACT

Mathieu Vigneau

Research Engineer

The platform's engineer evaluates the user's request and proposes the most suitable solution to his needs:

  • Advice and support of the user at the various stages of data processing and analysis
  • Hardware and software use support
  • Software training until users become autonomous
  • Development on request of specific scripts for the processing and analysis of large volumes of data
  • Support in the implementation of research and development projects in the form of collaboration

Cytometry

Cytometry

The platform allows the phenotyping of cells through the detection and identification of membrane and intracellular molecules. In order to purify a cell subpopulation, we also perform high throughput cell sorting, based on multi-parametric cell analysis. These subpopulations can then be studied for different parameters (transcriptome, proteome, in vivo transfer...).

RESTORE cytometry platform is a partner of the Toulouse Imaging Network Platform (TRI). It is certified ISO 9001 version 2015. The platform has a cell sorter, two analyzers and an image cytometer and offers a strong expertise on cells coming from solid tissues (adipose tissue, muscles, gums…). All the equipment is integrated in a L2 containment area.

The use of the equipment is open to research teams from public and private institutions, subject to acceptance of the projects by the manager.

expertise

CONTACT

Marie-Laure Renoud 2

Marie-Laure Renoud

Engineer

The platform's engineer evaluates the user's request and proposes the most suitable solution for his needs:

  • providing advice in the development of multi-color panels,
  • providing training to users,

  • assisting users in the analysis and interpretation of their results,

  • assisting users in the implementation of research and development projects, in the form of collaboration.

Pour les utilisateurs réguliers : Réservation directe

Imaging

Imaging

One of the challenges in biological imaging is to visualize biological structures and living organisms in three or four dimensions. CERT has a range of instruments and expertise to perform this type of analysis.

expertise

CONTACT

Corinne Barreau

Engineer
laetitia.pieruccioni

Laetitia Pieruccioni

Engineer

The platform engineers evaluate the user's request and propose the most suitable solution for his needs by :

  • providing advice in the development of multi-color panels,
  • ensuring the training of users,
  • assisting users in the analysis and interpretation of their results,
  • assisting users in the implementation of research and development projects, in the form of collaboration.

Mechanobiology-AFM-BioFab

Mechanobiology
AFM BioFab

The MecanoBioFab develops original technological tools to support the institute's researchers in both the field of mechanical properties measurements on cells and tissues and in the field of manufacturing 2D and 3D supports for the elaboration of in-vitro models.

The AFM Mechanobiology platform develops new automated approaches to acquire the mechanical properties of cells, cell populations and tissues.

expertise

CONTACT

Childerick Severac

PhD - IR CNRS

The platform engineer evaluates the user's request and proposes the most suitable solution for his needs. He :

  • provides advice in the design of experiments,
  • trains the users,
  • assists users in the analysis and interpretation of their results,
  • assists users in setting up research projects through collaboration with CERT.

Genomics & Transcriptomics

Designed by kotkoa (DNA) and starline (background) / Freepik. Modifié

Genomics &
Transcriptomics

Our platform is specialized in genome and transcriptome studies and offers a wide variety of services to research teams.

expertise

CONTACT

emmanuelle arnaud

Emmanuelle Arnaud

Transcriptomics Engineer
odilemondesert

Odile Mondésert

Genomics Engineer

The platform's engineers evaluate the user's request and propose the most suitable solution for his care by :

  • providing advice in the development of experiments,
  • training users,
  • assisting users in the analysis and interpretation of their results,
  • accompanying users in the implementation of research and development projects, in the form of collaboration.

Physioxia & Hypoxia

Physioxia
& Hypoxia

Within tissues, the oxygen level is much lower than that of the atmosphere in which cells are conventionally grown (21% O2). In order to study cell metabolism in conditions close to those present in tissues, it is essential to grow them in an oxygen-controlled atmosphere. Cell oxygenation, at the heart of Inserm and Restore's research, has been awarded a prize in 2019.

expertise

This incubator mimics the physiological oxygenation conditions of cells or tissues throughout their culture, without fluctuation of the atmospheric environment. It allows the study of different populations of stem cells in conditions close to those encountered in vivo and to lead to new therapeutic leads. (complete article).

The X-Vivo apparatus (Biospherix) is an enclosure with a fully controlled oxygen atmosphere. It allows, thanks to its different modules, to realize simultaneously different cultures with different levels of oxygen (1%, 2%, 5%, …) according to the experimental demands and this throughout the culture:

  • 6 independent incubators with specific oxygen control

  • 2 independent working modules with specific oxygen control

  • 2 independent transfer airlocks

  • 1 module with a microscope

CONTACT

Métabolisme, adipocytes, métabolomique, fluxomique, traçage isotopique in vitro/in vivo, culture cellulaire en hypoxie, activité mitochondriale

Jeanson Yannick

Yannick Jeanson

PhD- Ingénieur Inserm

Vieillissement, fragilité, cancer, métabolisme redox, hypoxie, flexibilité métabolique, lipides, fibroblastes, cellules souches mésenchymateuses

ADER Isabelle

Isabelle Ader

PhD- Chargée de recherche Inserm

A researcher and an engineer, both experts, evaluate the user's request and :

  • Authorize access to the equipment after prior training
  • Advise for the design of experiments in hypoxia
  • Realize as a service your entire hypoxia experiment

Fluxomics

Fluxomics

In recent years, the study of metabolism has been at the heart of physiology and health issues. The applications are numerous and include the fundamental understanding of physiology and pathologies, the identification of new therapeutic targets and individualized post-therapeutic follow-up. The ability to understand metabolism is therefore a major challenge in the understanding of aging and in the fight against diseases such as cancer.

As part of a joint initiative between RESTORE, CRCT and the MetaToul platform, CERT houses an in vivo fluxomics facility that includes:

  • two modules allowing the realization of isotopic tracing experiments (stable isotopes: 13C, 15N, etc) in vivo or in vitro
  • the equipment necessary for the collection of samples and the extraction of metabolites
  • a culture chamber under controlled oxygen pressure to understand the effect of oxygen partial pressure variations on metabolism
  • a respirometry tray to measure oxygen consumption flows

Metabolome, lipidome and isotope labeling analyses are performed on the MetaToul platform, which has an instrumental park (mass spectrometry, NMR) and unique expertise in this field in France. The whole set-up and the associated expertise represent also a unique configuration in France for in-depth studies of metabolic dynamics at different scales (from the cell to the whole organism).

expertise

CONTACT

Métabolisme, adipocytes, métabolomique, fluxomique, traçage isotopique in vitro/in vivo, culture cellulaire en hypoxie, activité mitochondriale

Jeanson Yannick

Yannick Jeanson

The platform engineer evaluates the user's request and proposes the most suitable solution for his needs. He :

  • provides advice in the development of experiments,
  • trains the users,
  • assists users in the analysis and interpretation of their results,
  • assists users in the implementation of research and development projects, in the form of collaboration.

Models of aging

Nothobroanchius

Models of aging

The regeneration of tissues and organs represents a major cognitive and medical challenge. The objective of our institute is to understand some of the underlying mechanisms to improve/restore regenerative capacities in adults.

The institute offers expertise in several models of aging, particularly in fish such as Brachyodanio rerio and Nothobroanchius furzeri.

These species were chosen mainly for their homology with the phenomena studied in humans (physiological, clinical…), for the technical tools that can be implemented (genetic tools allowing for example access to mutated lines, physical tools such as imaging, surgical tools allowing the development of models and the use of biomaterials) as well as for the bibliographic data related to these species.

expertises

CONTACT

Foie, tissu adipeux, macrophages, métabolisme, inflammation, vieillissement

user

Jean-Philippe Pradere

L’ingénieur de la plateforme évalue la demande de l’utilisateur et propose la solution la plus adaptée à ses besoins. Il :

  • assure le conseil dans l’élaboration des manipulations,
  • forme les utilisateurs,
  • assiste les utilisateurs dans l’analyse et l’interprétation de leurs résultats,
  • accompagne les utilisateurs dans la mise en place de projet de recherche et développement, sous forme de collaboration.