Quality Control

We use the NanoDrop-1000 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 much dilute samples (< 50 ng/µl).

We use the Agilent 2100 Bioanalyzer to analyze the integrity of nucleic acids. Total RNA samples can be processed on either a Nano chip, Pico chip or a Small RNA kit, 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. Useful information about QC measurements using the NanoDrop and the Bioanalyzer can be found here.