I wanted to make a stable cell line that expresses an shRNA. So I cloned shRNA in a retroviral vector. I wanted to know if I can know where exactly would it integrate in cell genome as it retorviral. Can I track it? I mean, can I use some tag or marker gene that I'll clone in the same vector upstream shRNA promoter or so?
I don't think that a 'tag' or a 'marker' will tell you where (on the 'sequence' level) the genomic integration location at. In plants, Agrobacterium can mediate transgenes insertion. To figure out the integration location of these transgenes, one can PCR and sequence the transgene neighboring region (genomic region) by using Inverse PCR (IPCR) or other PCR method (see attached picture). Once you have the neighboring sequence and the genome of your organism is sequenced, then you can find out where your 'transgene' locates.
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