At four different steps prior to microarray hybridization quality controls are performed:

1) The integrity of total RNA is examined on an Agilent 2100 Bioanalyzer. This is basically a miniaturized electrophoresis device for nucleic acids;  results are depicted as an electropherogram or in a "gel view mode". For examples of "perfect" RNAs and RNAs degraded to varying degrees see here or download this file: ppt (345kB).

2) cDNA yield is determined photometrically (A260).

3) cRNA yield and the efficiency of Cy3- or Cy5-incorporation are determined photometrically (A550 or A650 /A260).

4) The distribution of cRNA fragments is analyzed on Agilent 2100 Bioanalyzer. For examples see here or download this file: ppt (110kB).