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Services – BluePippin (SageScience)

• BluePippin Cassette kits

• Online Submission Request

• Physical Submission of Samples

BluePippin (SageScience) The BluePippin (jpg) has the capabilities of the Pippin Prep, plus pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer with no possibility of cross contamination in the cassette. Gel cassettes for DNA selections are available in 4 agarose concentrations to provide a full range of size selection options between 100bp up to 50kb. Run times range from ~30 minutes (small fragments) to several hours (pulsed-field runs for very large DNA fragments). Visit SageScience's website for product specifications of its BluePippin kits.

BluePippin Cassette kits

Kits contain 10 disposable pre-cast gel cassettes; all necessary standards and reagents are included. Cassettes that use internal markers have 5 samples lanes; cassettes using external markers have 4 sample lanes. Reimbursement is "per lane used". Before submitting a request for size-selection by BluePippin cassettes, please ask if the desired kit is in stock; the most common kit stocked by the Core is in bold below.
  • 3% agarose, 100-250bp (Internal marker)
  • 2% agarose, 100-600bp (Internal marker)
  • 1.5% agarose, 250bp – 1.5kb (Internal marker)
  • 0.75% agarose, 1-50kb (External marker)
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    Online Submission Request

  • Log In to the website, click "Services", and then "Bluepippin":
    • Form: Make all necessary 'selections', including the 'check box', and click 'submit'. Please note that "Quantity" for this assay refers to the number of lanes required to process all the samples.
    • Size-Selection: Depending on cassette type and targeted sizes, collected fragment sizes (as determined on the Bioanalyzer) may differ from expectations by up to 5-15% (for details, see BluePippin Cassette Specifications). Further, we have seen that the size ranges collected on the 1.5% gels tend to run smaller than expected, while they run larger than expected on the 2.0% gels; these biases must be taken into account if you need to avoid a specific fragment size.
    • Product yield: Maximum yields are obtained with broad vs. tight size selections. If needed, following collection of the DNA from the elution modules, additional yield may be obtained by collecting buffer added to the emptied elution modules (albeit, at the cost of reduced product concentrations).
    • Sample-related information: In the "Client Memo" box, provide all information necessary to process your samples (e.g.: target size for Tight collections vs. minimum/maximum fragment size for Range collection; maximize recovery (see below); and "special requests").
    • Special Requests: We might be able to adjust protocols to handle cases where your desired size-selections conflict with the normal protocols. For example, suppose you wish to target 150-600bp using the 2%-gel cassettes, which normally co-migrate two marker bands (50-bp, 150-bp) with the sample in each cassette lane (i.e., they use 'internal' markers). However, by sacrificing a sample lane, we can run the Marker solution as an "external marker", thereby allowing us to start collecting your DNA at 150-bp in the other 4 lanes. If your sample requires special handling, please contact the Core to discuss the situation and then provide the necessary information in the 'Comment' field for your online submission.
    • Maximum Recovery: Typically, a few µl of sample remain in the elution module after collecting the elution buffer. If you request "Maximum Recovery", 40 µl of TVLE (10 mM Tris, 0.05 mM EDTA) will be added to the elution well, mixed by pipetting, and collected. In this case, you will receive ~70 µ/sample vs. the normal ~35 µl/sample. Naturally, the DNA concentration will be considerably reduced and the buffer concentration (see below) will be altered. If necessary, since the second collection is done with TVLE, you can subsequently restore the DNA concentration by means of the SpeedVac.
    • Processed Samples: The electrophoresis buffer is 50 mM Tris, 30 mM TAPS, and 0.1 mM EDTA. However, as EDTA does not rapidly equilibrate across the ultrafiltration membrane of the elution module, the final EDTA concentration of eluted samples is elevated to ~1-2 mM. Of course, in 'maximum recovery' situations, the buffer concentrations are lower.
  • If you make an error in your request, you may revise that request if you do so before we begin processing it.
  • You will receive an automated email when your samples have been processed; your size-selected samples will be in the refrigerator (either for pickup or for further analysis on the Bioanalyzer, as per your instructions).
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    Physical Submission of Samples

  • Sample concentration:   See kit specifications for the minimum and maximum allowable concentrations. In general, for sheared genomic DNA, concentrations must be <2 µg (1.5%-agarose cassettes) or <5 µg (all other cassettes), while the minimum concentration is 15 ng.
  • Sample volume:   Bring DNA samples to 30 µl with 1X TE.
  • Sample buffer:   ≤80 mM monovalent ions.
  • Sample purity:   For best results, samples should be de-proteinized to prevent binding of the separated DNA to the ultrafiltration membrane at the back of the cassette's elution module.
  • Tubes:  individual tubes (vs. strips) are preferred; for best results, use "Lo-Bind" tubes (e.g., Eppendorf Lo-Bind or Axygen Maxymum Recovery tubes).
  • Label Submission:  Upon successful submission of your online request, the 'Submission #" will appear under your "Submission History". Then, label the tube rack itself with:
    • Submission #;
    • Date;
    • PI's Last Name; and,
    • Submitter name or initials.
  • Delivery site:  Transfer tubes to a Genomics Core rack (taking your own rack back to your lab), and put samples in the Mini-fridge (by sink) in the Genomics Core (A628 Life Science Annex).

    [Note: If the Core is locked, put your samples in the plastic "After-Hours" GC drop-box located in the adjacent Cold Room (beside sink, Rm. A650).]

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