DNA ext from paraffin-embedded tissue ... a dilemma ! - FFPE tissue refuse to lyse strange whitish clumps formed!! (Oct/06/2010 )
i was working on DNA ext from paraffin archives for breast cancer MSc project. i used commercial kit called pinpoint from zymo research. tissue appeared to be lysed i put it in freezer for some time then i came back to complete the purification steps when i found most of the samples have not lysed well. i reincubated them but strange thing happened!! some bulky whitish gelatinous clumps formed which wasn't there before i took these clumps n' incubated them with lysis buffer this time using Qiagen now maybe for 3 days but these weird masses did not lyse i even crushed some of them with liquid nitrogen but seems no use. this is my final semester in MSc and this problem has made a worst nightmare for me i'm so confused what could be this whitish clumps and how did they form ... plz help out! thanx in advance
whitish lumps in a DNA extraction sounds like the proteins and lipids coming out of solution to me, these are waste products that are usually discarded anyway, the DNA should still be in the supernatant! Those precipitates usually only form in the step after the lysing, but I don't know what freezing the lysed solution would do, perhaps they came out of solution early due to tthe freezing.