DNA and RNA extraction from the same sample is needed to compare genomic and transcriptomic data reliably. Usually, this is done by splitting the sample into two separate reactions/tubes/containers. The extractions are then processed separately. Thus, DNA is extracted from one piece of the sample, while RNA is extracted from the other piece.
Conventional methods have two major disadvantages: First, the amount of nucleic acids that can be extracted from the sample is cut into half. Second, because DNA is extracted from one group of cells, and RNA is extracted from a separate group, there can be differences in the properties of the cell sources.
The patented AllPrep DNA/RNA FFPE procedure incubates FFPE tissue samples in a lysis buffer that releases RNA into the supernatant and leaves DNA in the pellet. The RNA and DNA are then purified in separate tubes but within the same automated run using one cartridge in the EZ2 Connect instrument. This way, DNA and RNA can be isolated from as many as 24 samples, all at the same time.
Extended crosslink removal at high temperature reverses more crosslinks, but it also increases nucleic acid fragmentation. RNA is more susceptible to heat-induced fragmentation than DNA – but it is also less affected by crosslinks.
Therefore, the optimal conditions for decrosslinking DNA and RNA are different.
By generating separate lysates for RNA and DNA, the EZ2 AllPrep DNA/RNA FFPE workflow allows optimal crosslink removal conditions for each nucleic acid type.