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)
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).
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.
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.