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Microarray Analysis Service (SAM)

The Microarray Analysis Service (SAM) core facility from IMIM (Hospital del Mar Medical Research Institute), using the Affymetrix GeneChip® platform, offers an integrated service for expression, cytogenetic and genomic studies to both public and private organizations.

SAM scientific and technical core facility provides support to researchers for any task, from basic research to clinical diagnosis. The experimental services offered are sample quality analysis, quantification and microarray process. Experimental design consultancy, statistical data analysis and orientation to its biological interpretation with specific tools are also included.

Uses

Genic expression studies
• Discovery of biomarkers involved in biological processes.
• Gene expression profile studies.
• Detection of genes and pathways involved in diseases and pharmacological treatments.
• Pharmacogenomics and toxicogenomics studies.
• Alternative splicing detection.
• Dose-effect studies.
• Classification of samples based on gene signatures.
• Predictive models associated with genes.
• miRNA analysis.
• Microarray analysis of degraded samples (ex: FFPE) and low quantity samples (from 500pg of total RNA).

Genomic studies (cytogenetics, CN – Copy Number and SNPs)
• Detection of DNA gains and losses.
• Copy number estimation for the identification and diagnosis of genetic diseases.
• Molecular karyotyping.
• Loss of heterozygosity (LOH), uniparental disomies (UPD) and mosaicism.
• SNPs genotyping.
• Population genetics.
• Genome-wide association studies.
• Microarray analysis of FFPE samples

Integration studies
The integration of expression and genomic data is a complete and effective approach to investigate the pathophysiological mechanisms involved at all stages of disease.

Offered services
• Experimental design advising.
• DNA / RNA quality control analysis.
• DNA / RNA /miRNA quantification.
• Sample processing, microarray hybridization and scanning.
• Image quality analysis.
• Data quality analysis.
• Statistical data analysis, even if data was obtained in an external lab.
• Orientation to data interpretation with pathway analysis, Gene Ontology (GO) and specific tools. We provide functional analysis with Ingenuity Pathway Analysis (http://www.ingenuity.com)

Equipment
• Affymetrix Research Platform: GCS3000 with autoloader
• Affymetrix Diagnostics Platform: Molecular Diagnostic System Model GCS3000DX2
• Agilent Bioanalyzer 2100
• NanoDrop 2000 Spectrophotometer.
• Qubit Fluorometer
• Termociclador GeneAmp PCR System 9700 (gold block)

Available arrays

Expression arrays
• Human Transcriptome Array 2.0
• Human/Mouse/Rat Gene 2.0 ST Array
• Human/Mouse/Rat Exon 1.0 ST Array
• Human/Mouse/Rat Gene 1.0 ST Array
• Model and applied research organisms Gene 1.0 ST Array
• PrimeView™ Human Gene Expression Array
• 3' IVT Arrays (HG-U133 family & others)
• Almac Xcel Array

Cytogenetics, SNPs & CNVs arrays
• Genome-wide Human SNP Array 6.0
• Cytogenetics Whole-Genome 2.7M Array
• CytoScan HD Array
• CytoScan 750K Array
• OncoScan Array

miRNA Arrays
• miRNA 3.0 Array
• miRNA 2.0 Array

Lara Nonell Mazelon
Data analysis responsible
Tel: 93 316 05 77
Access Procedures

To make a service request an e-mail must be sent to sam@imim.es. In general, a service request follows the following steps:
1. Interview
2. Service request (application user's registry)
3. Cost estimation approval
4. Sample delivery
5. Sample quality control
6. Sample processing and microarray hibridization
7. Data analysis
8. Report delivery

Office hours: Mi-Fri 10-14h /Thu 15-18h

Assurance of quality

ISO 9001:2008 in progress

Type
Public