I have extracted total RNA from peripheral blood mononuclear cells (PBMCs), including RNA molecules greater than 18 nucleotides (microRNAs) and then I have checked the integrity by the Bioanalyzer. I have obtained bad results in some samples (RIN
I would think that this is very unlikely. The abundance of microRNA compared to ribosomal RNA is low. Also, I have extracted RNA from PBMCs and other hematopoietic cells, and so far usually have good RIN values.
The cases where RIN have been bad were in a few cases when I extracted RNA from low number of cells (a few hundred) or I technically messed something up and the samples were slightly degraded.
+1 to everything above.
Also, RIN is calculated based on the ratio of 2 peaks: the 28S to 18S. Are you sure that your bioanalyzer has accurately identified those peaks? (you can manually adjust the "line" which delineates these peaks using the bioanalyzer software) Have you checked that the baseline has been set accurately?
A thread which has examples of good and bad traces is here: http://seqanswers.com/forums/showthread.php?t=3898
The example from jcotney is useful in showing what a "normal" trace for a mouse/human should look like. If you see such a trace, but the "lines" at the bottom of the peaks are not in the correct location, you should adjust them manually to get a proper RIN.
Darya is right in that 28s/18s is the basis for RIN. However, RIN also takes into account the baseline for each peak and whether it is straight or sloping; and the baseline component I find to be less reliable. No harm in looking at both values separately. We use two thresholds for inclusion of tumours in big studies and found that passing either one (RIN or ratio) is equally good for subsequent RT-qPCR, microarrays and RNA-seq. e.g. samples that have a decent ratio but a so-so RIN are still good.
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