I am working on a project to measure the gene expression on rare cells with a white blood cell background by using the digital PCR technique. The first thing is I need to make sure the tested gene have no expression on WBC.I extracted RNA using the PicoPure RNA extraction kit and recommended Purelink DNase set. Then in ddPCR I used the extracted RNA as template to observe if there is genomic contamination. However, I always can get several positive droplets which indicate there is genomic contamination even the positive droplets are not too much. How can I remove the genomic contamination completely since It is quite important in detecting gene expression level on very rare cells.
Thank you, Mikael. I added some no template control in the same run, and no positive droplet shown in NTC wells. That may indicate there is no contamination in the master mix or primers/probes. Yesterday I tried to extend the incubation time of DNase or treat twice, still I can found 1 or 2 positive droplets. Someone told me it can only remove 95-99% DNA with DNase, I just wonder if this is true.
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