Ecogenomics platform

UMR INRAE-UL 1136 IAM

Manager: Annegret Kohler

The ecogenomics platform provides devices and tools to study forest ecosystems and tree-microbe interactions. This includes sanger sequencing, digital PCR, quantitative PCR, quality control of nucleic acids 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 INRAE Grand Est-Nancy in Champenoux.

For general questions and questions related to genomic/transcriptomic projects contact Annegret Kohler (annegret.kohler@inrae.fr; phone +33 (0)383 394 072).
For questions concerning bioinformatics contact Emmanuelle Morin (emmanuelle.morin@inrae.fr; phone +33 (0)383 394 133).

Our confocal microscope and laser microdissection device were integrated into the SilvaTech plateforme recently. (https://www6.nancy.inrae.fr/silva/Plateformes/SilvaTech). Please contact the responsable manager directly.

Specificities:

The ecogenomics platform is part of the ecogenomics of interactions team UMR INRAE-UL 1136 IAM at INRAE Grand Est Nancy.

The ecogenomics platform has close relationships to the SilvaTech platform located at INRAE Grand Est Nancy, situated in the same building.

The Research Unit IAM belongs to the scientific center A2F. The A2F scientific pole groups 7 research laboratories from the University of Lorraine (UL), 2 of which are University research units, and 5 of which are associated with INRAE (as mixed University-INRAE research units or as University research units under contract with INRAE) or INRAE and AgroParisTech.
The A2F pole is part of the EFABA federative structure (Forest Ecosystems, Agroresources, Bioprocesses and Food) which includes all the units involved in LABEX TREE, the units of the AGROVALOR consortium (with the exception of the LSE), and some of the research units involved in the LUE IMPACT Biomolecules project. This interdisciplinary structure provides the means to interact with other research units within the university perimeter, which are also in the EPST (INRA and CNRS units). Research laboratories of the A2F scientific pole share more collective technological platforms.

List of equipments:

  • Microscopy
  • Quality control of nucleic acid samples
  • Sequencing
  • DNA detection and gene expression analysis
  • Bioinformatic ressources

Quality control of DNA and RNA

     

 

 

 

 

 

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.

Rototgene

Qiagen Rotor-Gene

Bioinformatic resources

Biocomp cluster is composed of :

  • one head node : DELL R630, 2x E5-2620 (8 cores), 32Gb RAM
  • one storage node : DELL R740xd with 12 x 4Tb disks

And 8 compute nodes :

  • 2 DELL R630, Intel Xeon E5-2680 v4 (14 cores) with 128Gb RAM
  • 1 DELL R640, Intel Xeon Gold 5120 (14 cores) with 128Gb RAM
  • 3 DELL R640, 2 x Intel Xeon Gold 5218R (20 cores) with 128Gb RAM
  • 2 DELL R640, 2 x Intel Xeon Gold 5218R (20 cores) with 512Gb RAM

SLURM is the native job scheduling system on the cluster

Funding: INRAE, Region Grand Est, FEDER