Genomics

The philosophy of this Unit is to provide full services to both internal and external customers. By full services we understand carrying out the whole analytic process: starting with the experimental sample (total RNA, genomic DNA), we carry out all the genomics steps, including technical advice about the design of the experiment, quality control of the samples provided, microarray analysis, and a standard bioinformatics analysis. The facility itself and its experimental protocols have been certified by ISO9001. The Occupational Health and Safety Management System of the facility has been also certified using the OHSAS18001 system.

In this Facility we provide complete services for:

• DNA Sequencing
  • Sequencing of DNA contained in plasmids or PCR fragments using ABI-3130xl sequencer (Applied Biosystems). This system is able to do both genotyping and SNPs analysis. Genomics studies using Affymetrix technology.
• Analysis of expression profiles using Gene Chip System of Aff ymetrix in different organisms.
• Analysis of expression profiles using Gene ST System of Affymetrix in different organisms.
• >Analysis of expression profiles and splicing alternative using Exon ST System of Affymetrix.
• Identification of regulatory promoter sites by inmunoprecipitation (ChIP on chip) and other kind of studies which involve complete genome.
• Analysis of polymorphisms (SNPs) and copy number studies.
• Analysis of miRNAs and its precursors.
• Printing and processing home-made chips:

  We provide a system to prepare home-made microarrays using the MGII Arrayer of Biorobotics. The samples are provided by the user (oligonucleotides, cDNAs, DNA cloned in BACs, antibodies, purified proteins or cellular lysates). These microarrays are hybridized using the automatized system hs4800pro (Tecan). Finally, the microarrays are scanned using the GenePix4000 system of Axon. Our Unit provides the files to be analyzed with bioinformatics tools.

Equipment

1. Analysis of RNA quality:
   • Agilent 2100 Bioanalyzer.
2. Platform for the analysis of Affymetrix arrays:
   • GeneChip Hybridization Oven 640.
   • GeneChip Fluidics Station 450.
   • Gene Array Scanner 3000 7G.
3. Platform for the manufacture of home-made arrays
   • Biorobot 3000 (Qiagen).
   • Arrayer (Biorobotics).
   • HS4800Pro Hybridization Station (Tecan).
   • GenePix 4000B (Axon).
   • Automatic sequencer, 16-capillary ABI Prism 3130xl (Applied Biosystems).