The RNA integrity number (RIN) is an algorithm for assigning integrity values to RNA measurements. The integrity of RNA is a major concern for gene expression studies and traditionally has been evaluated using the 28S to 18S rRNA ratio, a method that has been shown to be inconsistent. This inconsistency arises because subjective, human interpretation is necessary to compare the 28S and 18S gel images. The RIN algorithm was devised to overcome this issue. The RIN algorithm is applied to electrophoretic RNA measurements, typically obtained using capillary gel electrophoresis, and based on a combination of different features that contribute information about the RNA integrity to provide a more universal measure. RIN has been demonstrated to be robust and reproducible in studies comparing it to other RNA integrity calculation algorithms, cementing its position as a preferred method of determining the quality of RNA to be analyzed. A major criticism to RIN is when using with plants or in studies of eukaryotic-prokaryotic cells interactions. The RIN algorithm is unable to differentiate eukaryotic/prokaryotic/chloroplastic ribosomal RNA, creating serious quality index underestimation in such situations. Terminology Electrophoresis is the process of separating nucleic acid species based on their length by applying an electric field to them. As nucleic acids are negatively charged, they are pushed by an electric field through a matrix, usually an agarose gel, with the smaller molecules being pushed farther, faster. Capillary electrophoresis is a technique whereby small amounts of a nucleic acid sample can be run on a gel in a very thin tube. There is a detector in the machine that can tell when nucleic acid samples pass through a specific point in the tube, with smaller samples passing through first. This can produce an electropherogram such as the one in Figure 1, where length is related to time at which the samples pass the detector. A marker is a sample of known size run along with the sample so that the actual size of the rest of the sample can be known by comparing their running distance/time to be relative to this marker. RNA is a biological macromolecule made of sugars and nitrogenous bases that plays a number of crucial roles in all living cells. There are several subtypes of RNA, with the most prominent in the cell being tRNA (transfer RNA), rRNA (ribosomal RNA), and mRNA (messenger RNA). All three of these are involved in the process of