Ecogenomics platform

UMR INRA-UL 1136 IAM

Manager: Annegret Kohler

The ecogenomics platform provides devices and tools to study forest ecosystems and tree-microbe interactions. This includes confocal microscopy, laser microdissection, small-scale sequencer as well as computing server for bioinformatics analyses.

Terms and conditions of use of the equipment:
The ecogenomics platform is open Monday to Friday by appointment with the manager. It is located in building K at INRA Nancy-Lorraine in Champenoux.

For general questions and questions related to genomic/transcriptomic projects contact Annegret Kohler (annegret.kohler@inra.fr; phone +33 (0)383 394 072). For questions concerning microscopy you can also directly contact Aurelie Deveau (aurelie.deveau@inra.fr; phone +33 (0)383 394 088) and for questions concerning bioinformatics Emmanuelle Morin (emmanuelle.morin@inra.fr; phone +33 (0)383 394 133).

Specificities:

The ecogenomics platform is part of the Ecogenomics of interactions team UMR INRA-UL 1136 IAM at INRA Nancy-Lorraine.

The Research Unit IAM belongs to the scientific center A2F (Agronomy, Food & Forests), which includes six research laboratories in the federal institute EFABA (Forest Ecosystems, Agricultural Resources, Biomolecules and Food Industry).
The A2F center relies on strong partnerships with INRA and a partnership with AgroParisTech. The two major areas of the industry are (i) the forest and wood and (ii) agronomy and food industry. These axes belong to a competence center of the Ministry of Agriculture and Fisheries and the Ministry of Higher Education and Research, entitled FABELOR (Forest, Food Industry, Biotechnology, Environment in Lorraine). The Forest-Wood section is structured around the laboratory of excellence (LabEx) ARBRE.
The ecogenomics platform has close relationships to the other platforms located at INRA Nancy-Lorraine, in particular with PTEF situated in the same building.

List of equipments:

Microscopy

Confocal microscope LSM 780 Zeiss

confocal

Funding : INRA, Region Lorraine, FEDER

Epifluorescence microscope ApoTome 1.0 Zeiss

ApoTome

Funding : INRA, Region Lorraine, FEDER

Stereomicroscope SteREO Discovery Zeiss

StereoDiscovery

Funding : INRA, Region Lorraine, FEDER

Laser Microdissection system with optical tweezer: PALM Robot-Microbeam system Zeiss

Microdissection

Laser Microdissection allows the separation and collection of cells of interest out of tissue samples or cell cultures. The isolated pure cell populations are the ideal starting point for further molecular analysis as for example gene expression analyses via qPCR or RNA-Seq. Optical Tweezers use a highly focused laser beam to manipulate and sort cells in suspension, for example bacteria.

Funding : INRA, Region Lorraine, FEDER

Publication : Hacquard, S., Tisserant, E., Brun, A., Legué, V., Martin, F. and Kohler, A. (2013), Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments. Environ Microbiol, 15: 1853–1869. doi:10.1111/1462-2920.12080

automated in situ hybridization and immunohistochemistry InsituPro VSi (INTAVIS)

insitu

The InsituPro VSi represents the third generation in the INTAVIS InsituPro product line for fully automated in situ hybridization and immunohistochemistry on whole mounts, vibratome sections, thin sections on slides and cells on coverslips

One system for both – In situ hybridization and Immunostainings, Automation of related staining techniques, Processing of whole-mounts, vibratome-sections, glass slides and coverslips, Recovery of probes and antibodies.

-More equipment for microscopic sample preparation (like vibratome and microtome) is shared with the xyloscience platform and PTEF at INRA Nancy-Lorraine.

Funding : Region Lorraine, FEDER

Sequencing and gene expression analysis

-Roche 454 Junior sequencer

Roche

allows sequencing of up to 100 000 reads per run.

Funding : INRA, Region Lorraine, FEDER

-Real time qPCR machines

Chromo4

Biorad Chromo4

Rototgene

Qiagen Rotor-Gene

-Quality control of nucleic acid or protein samples

Nanodrop

Nanodrop 1000 Spectrophotometer

The Thermo Scientific NanoDrop 1000 Spectrophotometer measures 1 ul samples with high accuracy and reproducibility. The full spectrum (220nm-750nm) spectrophotometer utilizes a patented sample retention technology that employs surface tension alone to hold the sample in place. This eliminates the need for sample containment devices and allows for clean up in seconds. In addition, the NanoDrop 1000 Spectrophotometer has the capability to measure highly concentrated samples without dilution.

Qubit

Qubit 2.0 Fluorometer

A benchtop fluorometer that accurately measures DNA, RNA, and protein using the highly sensitive Qubit quantitation assays. The concentration of the target molecule in the sample is reported by a fluorescent dye that emits a signal only when bound to to the target.

Experion

Biorad Experion

The Experion automated electrophoresis station performs all  steps of gel-based protein and nucleic acid electrophoresis in one compact unit. It is completed by a priming station for automated chip preparation and a vortex station to ensure correct mixing of reagents.

Bioinformatic resources

cluster_biocomp

Funding : Région Lorraine

Biocomp cluster is composed of one head node (DELL R620, 2x E5-2630 (6 cores), 32Gb RAM), one storage node (DELL R720xd with 12 x 2Tb disks) and 6 compute nodes (DELL R710, 2 x X5675 (6 cores), one with 24Gb RAM and the other with 96Gb RAM; DELL R620, 2 x E5-2660 (8 cores), one with 384Gb RAM, one with 192Gb RAM and two with 64Gb RAM).
SLURM is the native job scheduling system on the cluster