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Objectives: The team includes expertise, know-how and equipments for the core facilities managed by GABI that are open to users outside of GABI :

The @BRIDGe Core Facilities (animal Biological Resources for Integrated and Digital Genomics, http://abridge.inra.fr);
The Electron transmission microscope of the MIMA2 multi-site electronic transmission microscopy imaging core facilities.
The Mass Spectrometry Platform (LC-MS) for fine milk phenotyping
Services and equipments are proposed for the conservation of biological samples to their analysis at the molecular, cell or tissue levels.

The total number of users varies between 120 to 170 per year.

Technological services and expertise

Biobanking services:

• BAC librairies: cattle, sheep, goat, horse, pig, rabbit, chicken.
• Conditioning, secured conservation, distribution of all types of biological samples except infectious material.
• 21 freezers at -80°C or -40°C,
• 2 nucleic acid robot extractors: ChemagicStar, extraction on magnetic beads (x24 ou x96), QiaCube, column extractions (x12),
• 8 instruments for the quantification and quality control of nucleic acids

@BRIDGe Genomics Services

• Agilent Station for microarray hybridization;
• Illumina MiSeq sequencing; Capture of targeted genomic regions;
• Quantitative PCR: Life Technologies QuantStudio 12K Openarray and TaqMan array cards; Digital PCR for absolute quantification with a BioRad ddPCR QX200 ;
• GeneSpring GX (Agilent) and Ingenuity Pathway (Ingenuity) analysis software for transcriptomes, GeneX (Multid) for qPCR.

Functional Analysis and Morphology at the cell and tissue levels (@BRIDGe)

• Histology: tissue fixation, slicing and staining; in situ hybridization on cryogenized tissue sections; immunohistochemistry, light-background virtual slides.
• A digital fluorescence/light-background scanner for virtual slides (Panoramic SCAN, 3DHistech), cassettes and slide printers (Primera), 2 ultramicrotomes (Reichert E – Leica UC6), 1 Leica immunohistochemical robot.
• Microgenomics by Laser Microdissection: production and genomic analysis of micro-and nano-quantities of material extracted from cells isolated from their tissue environment under morphological control.
• Laser Capture Microdissection System (ARCTURUS XT IR /UV), 2 cryostats, 1 SnapFrost.

Ultra-structural analysis of the cell and its organelles (MIMA2)

• Electron transmission microscopy platform with 2D and 3D analysis and reconstruction with a HITACHI 7700 electron microscope.

The Mass Spectrometry Platform (LC-MS) for fine milk phenotyping
The LC-MS platform of UMR GABI offers a method for profiling the 6 major proteins in bovine milk (caseins ∞s1, ∞s2, β and κ, β-lactalbumin and -lactoglobulin), based on the coupling between reverse phase liquid chromatography (RP-HPLC) and type mass spectrometry (ESI-MS).

This method (LC-MS) (without equivalent to date) allows the identification and quantification of genetic and splice variants as well as the different isoforms resulting from post-translational modifications (phosphorylation and glycosylation) of the 6 major lactoproteins. Most of their major degradation products can also be determined, including caseins and their complements (peptone proteoses) resulting from proteolysis by plasmin, the endogenous milk protease.

Activities and Networks

The fields of activity are structural and functional genomics, microgenomics, morphological and ultra-structural analyses.
The biobank and genomics and microgenomics facilities are part of the CRB-Anim national infrastructure supported by the 'Investissements d'Avenir' program since 2012, which forms the animal pillar of the "RARe-AgroBRC" research infrastructure for Agronomic Resources for Research.
Quality certification

• The @BRIDGe core facility is ISO 9001:2015, and NFS 96 900 certified for its biobanking activities. The biobank is approved by IBiSA and by INRAE as a Collective Scientific Infrastructure (ISC).
• The MIMA2 core facilities is approved as an ISC by INRAE

Team leader: Michèle Tixier-Boichard
Co-leaders : Claudia Bevilacqua > Microgenomics, qPCR ; Christine Longin > electron microscopy

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