Microarrays technologies

Microarrays technologies

Microarrays allow us to analyze expression profiles (mRNA and microRNA levels) and structural variation (DNA copy number) on a genome-wide level.

The Microarrays Unit is equipped with all the instruments to carry out microarray analysis with the latest version of Agilent technology and provides a full service, including:

  • Technical advice in experimental design
  • Quality control of starting material
  • Sample labelling and array hybridization
  • Raw data extraction and QC of the raw data
  • Data analysis is done by the Bioinformatics Unit at CRG

All critical steps of experiments are performed in ozone-free laboratory environment to safeguard dye stability.

We offer a range of options suitable for a variety of experimental questions:

  • Gene expression arrays
  • microRNA arrays
  • Whole genome arrays (CGH and CNV)

Please, contact us to inquiry about the latest versions of each array type. We will be happy to assist you (jochen.hecht@crg.eu, anna.ferrer@crg.eu)

Sample preparation guidelines:

RNA extraction method:
We recommend using column-base RNA extraction methods that co-isolate small and large RNA molecules (ex. miRNeasy kits from QIAGEN or mirVana™ miRNA Isolation kits from AMBION).

DNA extraction method:
We recommend using DNA extraction methods based on silica-membrane nucleic acid purification (ex. QIAmp DNA blood extraction kit and QIAmp DNA Mini kit from QIAGEN), modified salting-out precipitation (ex. Gentra Puregene from QIAGEN) or magnetic beads nucleic acid purification (ex. CHEMAGEN).

Starting material:
Agilent gene expression arrays: 100ng of total RNA (25ng if the amount of RNA is limited). The optimal concentration would be around 80ng/ul.
For microRNA arrays 100ng of total RNA is used. The optimal concentration would be around 60ng/ul.
For CGH-CNV arrays: 1 mg of genomic DNA The optimal concentration would be around 70ng/ul.

Please not that we will need extra 3-4ul of the sample for the quality control.

QC:
The quality of every RNA sample will be tested on the Agilent Bioanalyzer and by measuring the concentration and the A260/A280 and A260/A230 ratios on the Nanodrop. We recommend that all samples have a minimum RIN score of at least 7.0 , an OD (A260/A280) ratio value >1.8 and an OD (A260/A230) ratio>1.5.

The quality of every DNA sample will be tested by agarose gel electrophoresis and by measuring the A260/A280 and A260/A230 ratios on the Nanodrop. We recommend that all samples have an OD (A260/A280) ratio value >1.8 and an OD (A260/A230) ratio>1.9.