Affymetrix Microarrays Platform (PAM)

Introduction

  • PAM


Affymetrix® Microarrays Platform (PAM) is a service focused on DNA and RNA microarray solutions offered by Affymetrix, with the main goal to offer solutions towards a personalized medicine. We offer microarrays for expression and for cytogenetics studies, from the basic research to applied research and diagnosis.

PAM is an Affymetrix European Reference Group for Cytogenetic applications and participates annually in the Cytogenetic European Quality Assessment (CEQA). 

Molecular cytogenetics

Microarray studies can offer various solutions for cytogenetic applications:

  • Detection of whole genome gains and losses at a high resolution.
  • Analysis of whole genome absences of heterozygosity.
  • SNPs genotyping and genome-wide association studies.

RNA Analysis Solution

Gene expression profile studies on either human or mouse are suitable for:

  • Detection of genes and pathways involved in diseases, treatment responses and biological processes.
  • Predictive models based on gene expression profiles.
  • Pharmacogenomics and toxicogenomics studies.
  • Alternative splicing detection.
  • Classification of samples on gene signatures.
  • Analysis of miRNA.
  • Microarray analysis on compromised samples with degraded and/or low quantity samples.

Quality sample analysis

In addition, to the microarray procedure we also offer DNA and RNA quantification and quality control analysis.

High throughput qPCR

The Biomark HD system is a high throughput qPCR that runs IFCs in either real-time or end-point read modes, bringing PCR solutions to a range of applications. Dynamic Array IFCs contain a matrix of channels with integrated valves that partition samples and reagents into different chambers, where individual PCR reactions take place. The 48x48 Dynamic Array combines up to 48 samples and 48 assays, generating 2304 different assays in one single run. The 96x96 Dynamic Array combines up to 96 samples and 96 assays, generating 9216 different assays. In addition, the FLEXsix IFC incorporates six 12x12 partitions that can be organized in any configuration, in up to six separate experimental runs.

Applications:

-        Genotyping

-        Targeted Gene expression

-        Digital PCR

 

Equipment

  • Affymetrix Research Platform: GCS3000 with autoloader
  • Agilent Bioanalyzer 2100
  • NanoDrop 2000 Spectrophotometer

Petition procedure 

A service request follows the following steps (link)

1- Contact us for an interview with the PI and other participants in the study. Please see the Contact section.

2- Service request sending an e-mail to genomic.platforms@carrerasresearch.org and filling in the Service request form.

3- Quotation according the specific needs and type of users.

Type of users:

- Can Ruti Campus: Researchers from institutions of the IMPPC immediate surroundings (Institut de Investigació Germans Trias i Pujol and Hospital Germans Trias i Pujol; Institut de Investigació Josep Carreras, etc), or that belong to executive board institutions of the IMPPC Foundation (Universitat Autònoma de Barcelona, etc), as well as researchers who are involved in direct collaborations with IMPPC members and that pay through a shared source of funding.

- External Researchers from all other external public and private institutions.

4& 5- Once the quotation is accepted by the PI, samples will be delivered to the PAM filling in the Sample delivery form and following the samples delivery requirements. Sample extraction is done by the researcher.

6- The sample quality control is required to check that the input sample fulfill all the requirements.

7- Microarray procedure and sample hybridization.

8- Data analysis.

9- Delivery of the report by e-mail or in an interview discussing the results.

 

Contact

Plataforma Affymetrix de Microarrays (PAM)

Person in charge: Laura Palomo, Core Facility Superior Technician

IJC Building
Ctra. de Can Ruti
Cami de les Escoles s/n
08916 Badalona
Barcelona, Spain
(+34) 93 557 2807 (Mon-Fri 08.30-17.30)

FOR ENQUIRIES AND QUOTES
lpalomo@carrerasresearch.org 

 

 
NamePosition
Francesc SoléF_sole_3XCampus Research Director
Mar MalloMmallo_3xPostdoctoral Investigator
Nuri De HaroNuri de HaroCore Facility Technician
Jessica TijeroJessica TijeroCore Facility Technician

Documents and prices

For a quote for the service you require please send an email to genomic.platforms@carrerasresearch.org

Services

RNA Analysis Solution

RNA Analysis Solution includes whole transcript Expresion Analysis & profiling for both fresh and FFPE samples

- GeneChip® Human/Mouse/Rat Exon 1.0 ST

- GeneChip® Human/Mouse/Rat Gene 1.0 and 2.0 ST

- GeneChip® Human Transcriptome Array 2.0

- Almac Xcel™ Array 

3' IVT Expression Analysis

- GeneChip® PrimeView™ Human Gene Expression Array

- GeneChip® Human Genome U133 Plus 2.0

- miRNA Analysis

- GeneChip® miRNA 3.0 and 4.0 Array

Please see the Affymetrix for other arrays and other species.

Please check the list for a guideline of prices. 

 

Documentation

High throughput qPCR – Biomark HD

-        Genotyping: Genotyping involves the analysis of single nucleotide polymorphisms (SNP) variations in genomes across individual organisms. DNA SNP genotyping on the Biomark HD Module can be performed using assays based on Fluidigm'sSNPtype chemistry or Life Technologie'sTaqMan® technology.

-        Targeted Gene Expression: Real-time quantitative PCR (qPCR) is a powerful technique for quantifying changes in gene expression by producing millions of copies of specific, targeted regions of complementary DNA (cDNA) that has been reverse transcribed from messenger RNA (mRNA) and microRNA (miRNA). Real-time qPCR on the Biomark HD Module can be performed using assays based on Fluidigm's DELTAgene chemistry or Life Technologie'sTaqMan® dual-labeled probes technology.

-        Digital PCR: Digital polymerase chain reaction (dPCR) is a technique that quantifies nucleic acid sequences that are present in a DNA sample. Digital PCR typically relies on standard PCR techniques but increases their sensitivity by dividing a sample into hundreds of smaller reactions and performing a PCR assay on eachsample. Digital PCR applications include copy number variation studies, absolute quantification,mutation detection and study of loss of heterozygosity.