The BluePippin system uses dye-free, pre-cast gel cassettes to separate and extract desired DNA fragment size ranges from agarose. It enables size selection for fragment lengths between 90 bp to 50 kb using different gel cassettes. The BluePippin system can run pulsed-field gel electrophoresis programs and thus separate large DNA fragments. Depending on the type of gel cassette up to 4 or 5 samples/cassette may be run, with no possibility of cross contamination. Samples in standard buffers (e.g., TE, EB) are compatible with the gel buffer, but preps in high-salt environments (e.g., after excess concentration in a speed-vac) should be avoided.
The agarose cassettes available in the Core are:
0.75% for PacBio, external markers, S1 (< 20 kb), U1 (>30 kb)
1.5% internal markers, 250 bp – 1.5 kb
2% internal markers, 100 bp – 600 bp
3% for miRNA, internal markers, 90-250 bp
Please also see the BluePippin cassette reference chart from SageScience.
Our assumption is that we lose about 50% of the DNA of the desired lengths during a BluePippin size selection, thus a considerable amount of input material is required. We recommend starting with 1 to 5 ug in a max volume of 30 ul (although as low as 500ng in 30 ul is possible in some cases).
The BluePippin instrument is available both as a Core Service and to campus users as shared equipment, after training.