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.
Services
• DNA Sequencing. Sequencing of DNA contained in plasmids or PCR fragments using ABI-3130 xl sequencer (Applied Biosystems). This system is able to do genotyping and SNPs analysis too.
• Genomics studies using Affymetrix technology.
The main services includes in this categorie are:
1) Analysis of expression profiles using GeneChip System of Affymetrix in different organisms. The main arrays used are: – Gene Chip Human Genome U133 Plus 2.0 – Gene Chip Mouse Genome 430 2.0 – Gene Chip Rat Genome 230 2.0 Array – Gene Chip Arabidopsis ATH1 Genome Array – Gene Chip Drosophila Genome 2.0 Array – Gene Chip Yeast Genome 2.0 Array. For more information visit www.affymetrix.com
2) Analysis of expression profiles using Gene 1.0 ST System of Affymetrix in different organisms. The main arrays used are: – Gene Chip Human Gene 1.0 ST Array – Gene Chip Mouse Gene 1.0 ST Array – Gene Chip Rat Gene 1.0 ST Array
These arrays are a new version (2007) for analysis of expression profiles cheaper and more complete In this Facility we provide complete services for:
a) Analysis of expression profiles and genotyping using Affymetrix technology.
b) Printing and processing of home-made chips.
c) Sequencing.
d) Genomics-related techniques such as RT-PCR.
than GeneChip System. For more information visit www.affymetrix.com
3) Analysis of expression profiles and splicing alternative using Exon 1.0 ST System of Affymetrix. The main arrays used are: – Gene Chip Human Exon 1.0 ST Array – Gene Chip Mouse Exon 1.0 ST Array – Gene Chip Rat Exon 1.0 ST Array For more information visit www.affymetrix.com
4) Identification of regulatory promoter sites by inmunoprecipi-tation (ChIP on chip) and other kind of studies which involve complete genome. The main arrays used are: – Gene Chip S.pombe Tiling 1.0 FR Array – Gene Chip S.cerevisiae Tiling 1.0 FR Array – Gene Chip Human Tiling 1.0 R Array For more information visit www.affymetrix.com
5) Analysis of polymorphisms (SNPs) and copy number studies. The main arrays used are: – Gene Chip Human Mapping 250K NspI/StyI Arrays – Genome-Wide Human SNP Array 6.0 For more information visit www.affymetrix.com
6) Analysis of miRNAs and its precursors.The main arrays used are: – Gene Chip miRNA 2.0 Array For more information visit www.affymetrix.com• 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 or DNA cloned in BACs). 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
Analysis of RNA quality:
• Agilent 2100 BioanalyzerPlatform for the analysis of Affymetrix arrays:
• GeneChip Hybridization Oven 640
• GeneChip Fluidics Station 450
• Gene Array Scanner 3000 7GPlatform 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)The services of this Facility and the overall service program of the Genomics/Proteomics/Bioinformatics Program of the Spanish Network of Cancer Groups can be found at: http://www.rticcc.org/articulos/p3n/
Scientific Coordinator
Xosé R. Bustelo Tel.: 923 294 816E-mail: xbustelo@usal.es/ encarnaf@usal.
Location and contact
Unidad de Genómica
Centro de Investigación del Cáncer (CSIC-Universidad de Salamanca)
Campus Universitario Miguel de Unamuno s/n E- 37007 Salamanca (ESPAÑA)
María Encarnación Fermiñán BenitoTel.: 923 294 816E-mail: encarnaf@usal.es