Dear Authors, How is the agarose that was dissolved in water not affected by xylene during the dehydration process? Does it stay intact?

Thank you for your thoughtful question.

The 2% agarose solution in our protocol solidifies at Step B.4 and therefore is no longer in a “solution” state. Because it is in a gelled, solidified matrix, it is not susceptible to dissolution by organic solvents such as xylene.

Furthermore, due to this very property, agarose gels in the range of 0.5–5% have been successfully used as recipient-block material in FFPE workflows (e.g., TMA construction using agarose-paraffin blocks) — see Kim K.H. et al., J Pathol Transl Med. 2013;47(3):238-244.

We hope this explanation has addressed your concern and been helpful.