In my experiment I would like to isolate epithelial cells from intestine to do RNA seq. I tried by vigorous shaking of the colon at 37o C, in buffer (DMEM, EDTA, DTT, FBS) for 10 minutes, followed by centrifuge and followed by RNA extraction by qiagen kit.
But I am getting very low RIN 4-5 and there is contamination of some parasite sequence.
1. Can anyone please suggest how do i get pure epithelial cells from colon which in turn can help me to get good RIN(8-10), and without contamination in the sequence?
2. Why my RNA is getting degraded and giving me bad RIN( since the qiagen kit is very good for RNA extraction otherwise)
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