In order to obtain bands for the 5' end we are ordering the pfx taq that is recommended in the generacer kit and I will be running a control on this as soon as we receive it. I repeated the cloning reaction on the 3' ends obtained in PCR, but was unable to do the control because we don't have kanamycin. We were using ampicillin screening on the colonies. I cloned the PCR products I did have and a few colonies grew on each plate. To purify the colonies I performed a mini prep, using two different colonies from each plate. I nanodropped the results of the mini prep and do have ample DNA. Using the purified plasmids, I am now performing PCR to excise the DNA sequences in order to use them in sequencing.
Hopefully over the next month I will be able to perform sequencing on the 3' ends and overcome the challenges on the 5' ends. Unfortunately, oligo capping doesn't always work but I am still hopeful that we can find a way to get results with this procedure.
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