Services and applications:

• Differential analysis of gene expression in different species (human, mouse, rat). Array types:

  • Clariom S: Whole transcriptome analysis at the gene level. Broad coverage of >20,000 well-annotated genes.

  • Clariom D: Analysis of the complete transcriptome, allowing the detection of more than 540,000 transcripts, including genes, exons and alternative splicing forms that give rise to coding and non-coding RNA isoforms. It also allows the detection of low-expression transcripts.

  • Earlier versions of expression arrays (check availability).

The protocol can be initiated with RNA extracted from different types of samples: whole blood, cell cultures, fresh, frozen or formalin-fixed and paraffin-embedded (FFPE) tissues. For good quality samples (RIN ≥7) we start with 100 ng of total RNA. For degraded or low concentration samples, one can start from 100 pg total RNA for fresh or frozen samples, and from 500 pg RNA of FFPE samples.

• miRNA screening: Analysis of pre-miRNAs, mature miRNAs (human, rat and mouse), as well as human snoRNA and scaRNA. These studies can be performed independently (e.g., to look for biomarkers), but also are complementary to gene expression studies, as it is estimated that more than 30% of the translation of protein-coding genes is regulated by small RNAs.

Consult this guide for detailed information on expression microarrays.

• Genotyping arrays (Axiom) for large-scale studies in humans and different animal species. They are high-throughput tools (plate format) that allow screening of gene variants in large cohorts. Different array designs are available for various applications: Precision Medicine Diversity Array, Pharmacogenomics, Microbiome. Custom designs are also possible.

• Cytogenetic studies, with fresh samples or FFPE (OncoScan/CytoScan).

Our service is currently specialized in gene expression and miRNA array processing. We are open to discuss and implement other types of projects, especially those related to genomic analysis.

Please contact us if you are interested in carrying out any type of study (genomica@vhir.org).

Equipment:

• Affymetrix GeneChip System for cartridge arrays. Includes two hybridization ovens (640 and 645), two 450 fluidic stations and a 3000 7G scanner combined with a PC workstation incorporating the Affymetrix® GeneChip® Command Console® (AGCC) software. 

• Affymetrix GeneTitan instrument for array plates (16x, 24x, 96x, 384x). Robotic system combining hybridization oven, fluidic stations and scanner in a single instrument.