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I have tried to make cDNA libraries from FFPE tumor blocks (highly degraded RNA) using the 3' end RNA seq protocol provided by West lab. Here is the link for the same. http://med.stanford.edu/labs/vanderijn-west/Protocols.html After PCR enrichment, a gel purification step follows. My trouble was, the fragments always gave rise to a smear rather than a band between 200-300 bp. Can anyone provide any suggestions as to why this may be happening? Thank You

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  • $\begingroup$ RNAse contamination? $\endgroup$ – Luigi Dec 17 '14 at 18:27

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