Question: Is there a sequence preference during cDNA fragmentation?
Answer: We have not observed evidence of sequence preferences in the cut sites of the fragmentation enzyme from human and mouse samples. Therefore we do not expect the fragmentation enzyme to result in bias across Single Cell 3' libraries from mammalian species.
It is possible that species with extreme AT or GC composition will perform differently. However, it is the cDNA and not the genomic DNA itself that is fragmented after RT. Thus, the presence of very low complexity or repeat regions in the genome should not be a factor in fragmentation.
Products: Single Cell 3'