We used FNA paraffin-embedded hepatic tissues from our study population to evaluate some gene expression. But already we got week results in RNA extraction and also in RT-PCR. We extracted RNA by using manually home-design method, trizol mRNA extraction protocol, and also some commercially available mRNA extraction kits (such as Qiagen, Bionner, and Ferments) but unfortunately the yield was very low. Since the majority of FNA samples are necrotic or fatty change tissues which have low cellular intensity, the extracted RNA will be unfortunately low. Please let me know how can we do in order to improve the yield.
Have you tried Arcturus PicoPure Rna isolation kit? it worked for us. we used it for a low amount of cells from LCM samples. We never tried it on liver/FNA tissue but in general it gives good results when we have very low input material.
Thanks Billel. I have never had an experience with that kit. But all methods/kits we have used they had not any satisfactory results.
Since embedded in paraffin I'd recommend using the shortest PCR amplicon primers as possible. If using commercially available then maybe buy 2 or 3 or if designing yourself go for the shortest possible. Typically the RNA from a formalin-fixed paraffin sample is in the rarnge of 80-100 nucleotides.
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