DNA and RNA concentration
NanoDrop is used to measure concentration and purity of nucleic acids before starting a microarray experiment. The concentration of nucleic acid is dependent on what array to be used. OD260/280 should be close to 2.0 for RNA dissolved in water and 1.8 for DNA. OD260/230 should preferably be above 2. A lower ratio might indicate contamination, such as GITC or phenol residues from extraction. A low OD260/230 reading can also occur as an artefact in samples with low concentration (< 50 ng/µl).
Agilent 2100 Bioanalyzer is used to analyze the integrity of nucleic acids. Total RNA samples can be processed on either a Nano chip, Pico chip or a Small RNA chip, depending on the sample amounts and concentrations. The RNA Integrity Number (RIN) software algorithm allows the classification of total RNA, based on a numbering system from 1 to 10, with 1 being the most degraded and 10 being the most intact. Total RNA for expression studies needs to be of high and even quality.