VMSR Quality Control/Quantity Assessment

Because microarrays are so sensitive to RNA degradation, all samples submitted for microarray work are first analyzed for quality and quantity. By requiring this check at the beginning, we can simplify data analysis (by removing poor performers early) and help investigators potentially save a lot of money

RNA

Unless the PI specifically requests otherwise (in the Special Instructions of the submission sheet), the following steps will be performed as part of RNA QC/QA:

  1. The sample is quantified in 10mM Tris on the Nanodrop ND-1000 Spectrophotometer. In addition to concentration, this instrument reports the 260/280 absorption ratio, which can be an important indicator of hidden contaminants.
  2. The sample is then analyzed on an Agilent 2100 Bioanalyzer. The electropherogram it produces makes it easy to spot certain contaminants or degradation, and to calculate the 28s:18s ratio (Sample Report).

The primary determinant of RNA quality in the VMSR is the RNA Integrity Number (RIN), produced by a recent upgrade of the Bioanalyzer software. This is a number ranging betweeen 1 (degraded) and 10 (intact). For microarray work, we recommend that all samples have a RIN of at least 7.0. The RIN is superior to other single measures of quality (such as the 28s:18s ratio) because it considers the entire electropherogram, rather than just one or two points. There are occasions, however, where the software refuses to assign a RIN. This does not mean that your RNA is bad! In this case, we advise investigators to examine the electropherogram, 260/280 ratio, and 28s:18s ratio to make a quality determination. If you need help with such a case, please contact us.

DNA

DNA submitted for a Genotyping project does not undergo a separate QC step - investigators should ensure the purity and cleanliness of their sample before submission. The VMSR does accept DNA for QA/QC as part of Quality Control projects, however. Unless a specific request is made in the Special Instructions of the order, the sample will simply be spec'd on the NanoDrop in Tris, as above. Bioanalysis will not be performed.