Bioanalyzer Data Interpretation
Each lane contains a marker along with your sample. The marker is used to align the samples. The concentration and sizing is determined from the standard ladder loaded in lane one.
The 28S/18S ratio may be indicative of problems with the RNA, but not always. Even though the ideal ratio is 2.0, the bioanalyzer rarely reflects this ratio. If the ratio is greater than 2.0 it may indicate the presence of sheared single stranded genomic DNA which can run around the 28S band. If the ratio is less than 1.0, there are usually definite degradation problems with the RNA. More important than an absolute number is the visual sign of degradation.
The Agilent Expert software assigns a RIN number to each trace. It assigns a number according to how much signal is found between the 5S and 18S band, between the 18S and 28S bands, and after the 28S band. An RIN number of 10 is perfect score or excellent RNA. The software does not always call RIN numbers for prokaryotic RNA and the RIN can be misleading for samples containing additional RNA bands such as those from chloroplasts or a symbiotic RNA.
Here are some Agilent articles about interpreting the RIN number
RNA Integrity Number (RIN) - Standardization of RNA Quality Control [PDF]
RIN Users Guide [PDF]
See some examples of Bioanalyzer traces [PDF] to help with data interpretation
Free software from Agilent is available to view your data (.xad file) on a PC.