Concentration and Quality Control
RNA concentration and purity
NanoDrop is used to measure concentration and purity of nucleic acids before starting a sequencing project. RNA dissolved in water should have OD260/280 close to 2.0 and OD260/230 preferably above 2. Lower ratios might indicate on contamination. A low OD260/230 reading can also occur as an artefact in samples with low concentration (< 50 ng/µl)
Caliper LabChip GX and Agilent 2100 Bioanalyzer are used to analyze the integrity of nucleic acids. The RNA Quality Score (RQS) for Caliper and RNA Integrity Number (RIN) for Bioanalyzer are software algorithms allowing 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.
DNA (FFPE) quality