What is the difference between the V-J and V-C reagent systems?
The V-J and V-C reagent systems refer to the location of the forward and reverse primers. The V-J system has reverse primers within the J gene, while the V-C reverse primers fall within the C region. Due to a large intron gap between the C and J gene, the V-C primers can only amplify RNA and not gDNA, as shown in the figure below. The forward primers for both systems begin in the V gene. Depending on the primer system ordered, then the amplified library would extend from either the third framework region (100/150 PER) or the first framework region (250 PER). To learn more about the different paired-end read options, please read our discussion on 100/150 PER vs. 250 PER.
The majority of our primer systems are compatible with RNA only; however, we do offer human TCR beta Illumina primers compatible with both gDNA (V-J primers) and RNA (V-J and V-C primers). Libraries that have been amplified using V-J primer kits can only be sequenced using 100 or 150 paired end reads (PER). Those libraries amplified using V-C primer kits can be sequenced using both 100/150 PER and 250 PER. Our Reagent Systems Interactive Guide will lead you through the selection process.
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