I have unstained FFPE tumor tissue, with the area of interest graphing on the back of the slides. The goal is to scrap off the area of interest, then extract both DNA and RNA.
What's the good order of the procedures?
Should I scrape the tissue first and then deparaffinized it? Someone also suggests me to bake the slides first and then scrape them.
Appreciate any pov!
Hi Yun,
Generally, when using the whole slide, scraping is done after rehydration (post-xylene etc.). However, based on your question it looks like you do not want the whole section.
Right at the beginning before deparaffinization, you could use a very sharp blade and then cut around the area you want. Don't scrape it or anything and leave the area still attached. Make sure you make a good cut through the tissue. This would the best time to make the cut when the slide is untouched and section is firm. Then you can do deparaffinization with xylene etc. and when you finish, the rehydration step, it will be easier to just remove that area by scraping, or use a regular sharp shaving blade to "lift" off the area.
Trying to cut after the rehydration step you will definitely be dealing with more fragile tissue and cutting may not be that easy. Don't do too much baking etc. this will jsut degrade the RNA/DNA that much more.
Hope this helps!
Good luck!
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