Transcriptomics platforms : Services
Experiment Design
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | help in building the experimental design of your microarray project in order to evaluate time and costs. | hybridation analysis | |
| Montpellier Génopole Microarray Facility | Site IGF/IGH: Design is discussed with the microarray team and users to evaluate the best experimental choice. | Website | |
| Nantes Microarray facility | For each new project, a specific proposal is discussed with the director of the platform | Website | |
| Toulouse | consultation | website |
Slide Production
| Name | Description | Link | |
| Montpellier Génopole Microarray Facility | Site IGF/IGH ready-to-use oligo microarrays or printing from cDNA or oligo collections |
Website | |
| Toulouse | Dendrislides | slides webpage |
Spotting
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | Several spotting services are offered to the user from microarray catalog to on demand spotting. | ||
| Montpellier Génopole Microarray Facility | Site IGF/IGH ready-to-use microarrays spotted on glass slide, or custom microarrays on demand by users |
Website | |
| Nantes Microarray facility | 2 types of chips on glass slide are produced : home-made chips with cDNA or oligos and "multidedicated-chips" (muscle, cancer) | Website | |
| Toulouse | glass slides, nylon membrans | spotters webpage |
RNA Extraction
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | All the advised protocol used ont the ENS Transcriptome plateform are available on the platform website. | protocols | |
| Nantes Microarray facility | Protocols of Molecular biology | Protocols | |
| Toulouse | yes | website |
DNA/RNA Measuring
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | For DNA and RNA measurement and quality control a Nanodrop and Bioanalyzer are on open access on our platform. | Materials | |
| Montpellier Génopole Microarray Facility | Site IGF/IGH nanodrop |
Website | |
| Nantes Microarray facility | Nanodrop | Website | |
| Toulouse | Nanodrop | webpage |
Protein Measuring
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | nanodrop spectrophotometer | ENS website | |
| Toulouse | Nanodrop | webpage |
RNA Quality Control
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | For DNA and RNA measurement and quality control an Agilent Bioanalyzer 2100 is on open access on our platform. | Materials | |
| Nantes Microarray facility | BioAnalyser Agilent | Website | |
| Toulouse | Agilent 2100 Bioanalyzer | webpage |
Labelling
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | The protocols used and advised by the ENS Transcriptome platform are freely available for download from the platform website. | protocols | |
| Montpellier Génopole Microarray Facility | Site IGF/IGH indirect labelling protocol |
Website | |
| Nantes Microarray facility | Direct labelling and Indirect labelling (Cy3, Cy5) | Protocols | |
| Toulouse | Cy3, Cy5, Alexa, P32, P33 | webpage |
Labelling Quality Control
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | A nanodrop spectrophotometer is available upon open access to quantify dye incorporation. | ENS website | |
| Montpellier Génopole Microarray Facility | Site IGF/IGH nanodrop |
Website | |
| Nantes Microarray facility | Nanodrop | Website | |
| Toulouse | Nanodrop (Cy3, Cy5), Scintillation Counter (P32, P33) | protocols online |
Hybridization
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | All the devices available for microarray hybridization are accessible on the microarray platform | ||
| Montpellier Génopole Microarray Facility | Site IGF/IGH Lucidea slidePro hybridizer |
Website | |
| Nantes Microarray facility | The microarray facility gives an access to the technologies Agilent, Amersham, and soon Affimetrix and Applied-biosystem | facility’s website | |
| Toulouse | Hybridization station "Ventana", Hybridization oven Agilent, manual hybridization | hybridization webpage |
Scan
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | Microarray slide scanners from Axon are available on the platform upon open access. In addition network License of GenePix are available on several open access computer to allow image analysis. | ||
| Montpellier Génopole Microarray Facility | Site IGF/IGH Axon 4200 Autoloader |
Website | |
| Nantes Microarray facility | 3 scanners : 2 Perkin Elmer (ScanArray one-slide and autoloader) and 1 Agilent | Website | |
| Toulouse | Axon4000 (slides 10 µm), Axon4100 (slides 5 µm), Storm (mbr 50 µm) | webpage |
Image Analysis
| Name | Description | Link | |
| AGScan | a micro-array image processing software | AGScan’s webpage | |
| ENS Transcriptome platform (Paris) | Microarray slide scanners from Axon are available on the platform upon open access. In addition network License of GenePix are available on several open access computer to allow image analysis. | ||
| Montpellier Génopole Microarray Facility | Site IGF/IGH: ArrayVision - GenePix |
Website | |
| Nantes Microarray facility | Genepix v5 | ||
| Toulouse | GenePixPro v6 (slides), XDotsReader (mbrs), ImageMasterArray (mbrs) | webpage |
Data Treatment
| Name | Description | Link | |
| ENS Transcriptome platform (Paris) | The platform helps users at various levels for microarray data analysis and interpretation. Tutorials, training sessions, bioinformatics tools and collaboration are available from the ENS platform according to the user choice. | ||
 |
GenoScript | GenoScript is an integrated environment for collecting, storing, querying and analyzing DNA chips data (micro- or macro-arrays) | GenoScript online |
| Mediante - Microarray open source database | An Anglo-French open-access oligonucleotide and bioinformatics resource for microarray analysis of the human and mouse transcriptomes | homepage | |
| Montpellier Génopole Microarray Facility | LIMS BASE | Website | |
| Nantes Microarray facility | Open-access bioinformatics tools for microarray analysis and annotation : MADTools | http://www.madtools.org | |
| Toulouse | BioPlot/BioClust | data treatment |
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