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Genomics platform

This Platform provides essential technologies dedicated to the quantitative and qualitative analysis of the nucleic acids in terms of base sequence, quality and expression levels.

Services and applications:

  • Real-time qPCR:
    • Relative and absolute quantification studies for transcriptional profiling
    • Analysis of gene copy number of genomic and viral DNA
    • Allelic discrimination studies (SNP detection)
    • Pathogen detection and identification trials
    • High Resolution Melting (HRM) for gene scanning

Assistance with experimental design, selection of probes and data analysis is also available. Customized services, including RT-qPCR design and performance, are available upon request.

  • Quantification and quality control of nucleic acids using microfluidic chips (Bioanalyzer ®):
    • RNA quality check (RIN algorithm) and quantification
    • Automatic separation, sizing and quantification of dsDNA fragments
  •  Fluorimetric quantification of nucleic acids (Picogreen ® for DNA and Ribogreen ® for RNA) highly specific and sensitive method, especially useful when:
    • Only a few cells are available for nucleic acid extraction
    • An extremely precise quantification is needed (i.e. for library construction in NGS)

For more information about different nucleic acid quantification techniques, click here.

  • Mouse genotyping, including:
    • DNA extraction from different types of samples (tail, ear…)
    •  PCR: customized for each individual project.
    •  Analysis by gel electrophoresis.
  • Detection of Corynobacterium bovis pathogen contamination from laboratory animal and environmental samples.
  •  Automated DNA sequencing by capillary electrophoresis. The service is available for different applications (i.e. resequencing, microsatellite analysis, difficult fragment sequencing) in several formats (tubes, plates). Universal primers are provided free of charge. Sequencing is managed by UAT and outsourced through an external partner. For more information, please click here.
  • Human cell line authentication service: human cell lines identity verification and detection of cross- contamination based on STR profiling, according to the ANSI/ATCC standards. STR analysis is performed using the kit GenePrint 10 System ® (Promega). A mouse marker can be added to check cross-contaminations. Serviced managed by UAT and outsourced through an external partner.

Equipment:

  •  Real-time PCR:
    • LightCycler480 (Roche): 96 and 384-well blocks.
  • Agilent 2100 Bioanalyzer:
    • DNA chips: DNA1000
    • RNA chips: Nanochip, Picochip
    • Users can bring their own chips to be processed at the UAT (i.e. High Sensitivity DNA or small RNA chips

Contact

For more information contact at genomica@vhir.org