In the FFPE samples, both DNA and RNA are fragmented. Someone does not use DNase I during RNA isolation of the FFPE sample. They found the DV200 was confusing.
Does DNA contamination affect RNA quality determination using RIN (RIN value or DV200)?
Hyde Chen
Yes, DNA contamination can affect RNA quality determination using the RNA Integrity Number (RIN). RIN is a commonly used method to assess the integrity and quality of RNA samples. It is based on the analysis of RNA fragment sizes using capillary electrophoresis.
If there is DNA contamination in an RNA sample, it can interfere with the RIN measurement because DNA fragments may be present alongside the RNA fragments. This can lead to an overestimation of the RNA integrity, as the DNA fragments may contribute to the total fragment length calculation.
To accurately determine RNA quality using RIN, it is important to ensure that the sample is free from DNA contamination. Various methods can be employed to remove DNA, such as DNase treatment or RNA purification protocols that include DNA removal steps. By minimizing DNA contamination, the RIN value can better reflect the actual integrity and quality of the RNA sample.
Yes, DNA contamination can affect RNA quality determination using RIN (RIN value or DV200). The presence of genomic DNA contamination in RNA samples can interfere with the calculation of RIN values or DV200, which are used to assess RNA integrity. This is because the presence of genomic DNA can lead to overestimation of the RNA concentration and can also affect the electrophoretic profile of the RNA sample, leading to inaccurate RIN values or DV200 calculations. Therefore, it is important to ensure that RNA samples are free from genomic DNA contamination before assessing RNA quality using RIN or DV200.
If someone does not use DNase I during RNA isolation of the FFPE sample, it is likely that the RNA sample will be contaminated with fragmented DNA. This can affect the determination of RNA quality using DV200, which is a measure of the percentage of RNA fragments that are longer than 200 nucleotides. The presence of fragmented DNA can lead to overestimation of the DV200 value, as the DNA fragments may be included in the calculation of the total RNA fragments. This can result in a confusing DV200 value, which may not accurately reflect the true quality of the RNA sample. Therefore, it is important to use DNase I during RNA isolation of FFPE samples to remove any contaminating DNA and ensure accurate determination of RNA quality using DV200.
https://worldwide.promega.com/resources/pubhub/methods-of-rna-quality-assessment/
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