The Pippin systems from SageScience allow for precise automated size selection of nucleic acid samples, sequencing libraries, and even protein samples. Our Core runs the PippinHT, which excels at high-throughput applications and also works with smaller sample amounts. The PippinHT sample sizing instrument allows precisely size-select DNA samples and sequencing libraries for up to twenty-four samples per single run. 

​The instrument belongs to our Shared Equipment – this means all UCD researchers can be trained to use this instrument. We are using the instrument for precise size-selection for all genomic DNA sequencing libraries prepared by our lab. This allows us to avoid generating redundant data for short insert library molecules (for which the reads would otherwise overlap); the precise size selection will further avoid lower quality data caused by library molecules that are too long. For example, the two customer libraries size selected for the optimal sizes (within the blue bars) removed about 50% of the library molecules that are outside of the optimal range. 

​The PippinHT agarose cassettes available in the Core and the size ranges in which samples can be sized: 0.75% from 6 kb up to 40 kb, high-pass 1.5% from 250 bp up to 1.5 kb, 2% from 100 bp up to 600 bp. For the the 2% cartridge selection intervals can be as small as 20 bp. The PippinHT loading volume is up to 20 ul of DNA dissolved in a low salt buffer (like EB, TE, or most enzyme buffers, or water). Samples in the typical Illumina library size range should contain at least 200 ng DNA in a 20 ul volume (detergent-free). Please refer to the PippinHT manual for more details.