Microarrays Analysis. Affymetrix Platform


Microarray technology contributes to the structural and functional analysis of the genome through the complementarities of nucleic acid bases and has been improved by Affymetrix.
Affymetrix GeneChip® microarrays are manufactured using in-situ synthesis of short oligonucleotide sequences (25 pb) on a small glass cartridge using light directed synthesis (photolithography).
This platform is continuously updated, has a high reproducibility and accuracy and is very robust. These characteristics allow direct comparison of data between laboratories and studies.


The Genomics Facility at CABIMER offers the following services to researchers from within and from outside the Centre: 

a) Gene expression profile analysis, using:

  • “3´Expression Arrays”, 11 probes per gene designed to detect the 3´ region of the transcripts and variants. For the conventional analysis of expression profiles based on predicted and well-annotated sequences from mRNA.
  • “Gene Array”, 26 probes per transcript spread over the sequence. For more complete studies of expression profiles (includes transcripts without polyA ends, microRNA…), more accurate (only well-annotated genes) and more cost-effective than the “3´ Expression Arrays”.
  • “Exon Array”, 4 probes per exon and 40 probes per gene (10 exons max). For gene-level and exon-level analysis.
 

b) Analysis of splicing events using “Exon Array”.

 

c) Analysis of microRNAs using
  • “miRNA Arrays”, for studies of mechanisms measured by miRNAs.

 

d) Analysis of regulation and full-length genes:
  • “Tiling Arrays” (Whole-Genome Array) which covers the whole genome and may be used for studies of Transcriptional Mapping and protein/DNA interactions (ChIP-on-Chip)
  • “Promoter Arrays” and “Encode Arrays” for the identification and study of promoter regions.

 


The specific GeneChips® for each organisms and analysis type are available from the Affymetrix Web site.


The Microarray Service includes the following items:

  • Recommendation and guidance for experimental design.
  • “Analysis of RNA Quality” (Bioanalyzer 2100) or of DNA as applicable.
  • Amplification and samples labelling (biotinylated).
  • Hybridisation and washing of Microarrays.
  • Reading of the arrays using the "3000 7G" model scanner.
  • Image analysis, fluorescent data quantification and Quality Control with Affymetrix software (raw data: *.CEL).
  • “Biostatistical Data Analysis” is included for expression arrays: fluorescent data processing (raw data), normalization of data using RMA algoristm, data analysis using the linear modelling for microarray data (limma) or Anova analysis that provide the fold change (treatment vs control) and the degree of confidence of the change (p-value),  and annotations of the different genes (Affymetrix identification number, gene symbol, name of gene and descriptions with the corresponding transcription access number).

 

 

The Facility gives advice of the possibilities and use of the different tools available for the subsequent data mining.


For sample recommendations and requirements, reception of samples and results, please refer to the Microarray User Guide.


For other questions, please refer to the Facility ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it or +34 954 467828).


Application form



Return to Services Offered