= RNA integrity
{c}
\b[RNA integrity] describes the preservation of <RNA> molecules relative to the molecular lengths and structures required by a stated analysis. <RNA degradation> can leave fragments containing short target sequences even after long transcripts have been broken. Integrity is therefore distinct from total RNA amount, chemical purity, correct <nucleotide sequence> and preserved biological activity.
An <electrophoresis> trace measures a size-dependent distribution of material. For a total-RNA preparation, <ribosomal RNA> contributes prominent features, while smaller fragments can alter the trace as degradation proceeds. The <RNA integrity number> introduced by <Andreas Schroeder> and colleagues combines several trace features into an algorithmic score. Its 1-to-10 scale is not a percentage: a score of eight does not mean that $80\%$ of every transcript is intact. A single ribosomal-peak ratio also differs from the multi-feature score.<The RIN: an RNA integrity number for assigning integrity values to RNA measurements by Andreas Schroeder and others>[Abstract, Feature selection, Discussion and Figure8]{ref}
An original cleavage model explains why assay length matters. Suppose cuts form a <Poisson process> along an RNA strand, with mean density $k$ cuts per nucleotide. A required segment of length $L$ is unbroken when it contains no cut:
$$
\boxed{\Pr(\text{required segment intact})=e^{-kL}.}
$$
At the stipulated density $k=0.001$ per nucleotide, a 100-nucleotide segment remains intact with probability $e^{-0.1}\simeq0.905$, while a 1000-nucleotide region survives with probability $e^{-1}\simeq0.368$. Detecting the short sequence consequently does not prove that the full long transcript survived. This is an illustrative independent-cut model, not a fit to a particular RNA sample or a conversion from an integrity score.
\Image[/rna-required-segment-intact-probability.png]
{title=Calculated survival of required <RNA> segments under an illustrative independent-cleavage model}
{description=The curve shows exp(-kL) at stipulated k=0.001 cuts per nucleotide. It is not an RNA integrity number calibration or an experimental assay-performance measurement.}
A motivating experiment is the 2008 comparison of RNA preservation during <laser capture microdissection>. <Mathieu Clément-Ziza> and colleagues measured RNA quality after staining and over the subsequent collection interval. Their tested argon-atmosphere and ethanol-based preparations stabilized the observed RNA quality for up to 90 minutes. Figure1 combines time comparisons with instrumental separation traces.<Stabilization of RNA during laser capture microdissection by performing experiments under argon atmosphere or using ethanol as a solvent in staining solutions by Mathieu Clément-Ziza and others>[Abstract and Figure1: time-dependent measurements, sample scrapes and Bioanalyzer readout]{ref}
An integrity assessment should state the specimen, handling history, measurement method and downstream requirement. <Quantitative PCR> directed at one short region and an analysis requiring an intact long transcript need not fail at the same degree of fragmentation. A stable total concentration cannot establish intactness, and a bulk quality score cannot certify every individual molecular species.
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