DNA/Library QC and Other Services Guidelines

The following guidelines apply to those submitting DNA or libraries for a la carte services.

All General Guidelines must be followed in addition to the guidelines specific to the requested service. Note that these discrete, a la carte services are included within some larger service requests. If you need library preparation or you have already prepared libraries for sequencing, please see the appropriate service guidelines.

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Sample Delivery Vessel - General Guidelines

  • Place in a 96-well skirted, translucent plate (e.g., Eppendorf twin.tec #00030129300).
    • Sample placement should be going down columns (A1,B1,C1…A2,B2,C2…) in contiguous wells (no skipping wells, rows, or columns unless “Blank” samples).
    • Plate should be sealed tightly with one of the following:
      • If shipping on dry ice, seal wells with tight-fitting 8-cap strips (e.g., Thermo Scientific #AB-0265)
      • If delivering from on campus, firmly seal wells with a clear adhesive seal (e.g., Bio-Rad Microseal ‘B’ Film #MSB1001).
    • Samples that are submitted in other containers will be transferred to a 96 well plate at the submitting lab’s expense. Please inquire for cost of transfer.

Sample Naming Conventions - General Guidelines

  • Each sample must be identified with a simple, unique identifier. If names have been used in previous submissions, don’t repeat in subsequent submissions.
  • The following conventions are strictly enforced:
    • 3-20 characters
    • A-Z, a-z, 0-9, dash (-) are the ONLY acceptable characters
    • Space, underscore, punctuation, and special characters are NOT ALLOWED
    • No replication

Sample Labeling Conventions - General Guidelines

  • All tubes and plates must include the following information.
    • PI name
    • Date
    • Sample name (tubes only)

Standard DNA QC (quantification and size analysis)

  • Follow ALL General Guidelines above.
  • This service provides fluorometric quantification and size analysis of dsDNA.
    • While certain fluorometric and size analysis assays are capable of quantification/detection of ssDNA, the assays we perform are intended for dsDNA.
    • Size analysis can only be performed after quantification.
  • If you intend to have additional services performed on your DNA or libraries after QC, please see the appropriate Guidelines for Submitting DNA for Library Preparation or Already Prepared Libraries.
  • Sheared/fragmented DNA, DNA from library preparation, amplification, enrichment, second-strand synthesis (cDNA), etc. is acceptable but MUST be in the range of 35 bp to 1,000 bp*.
    • * For DNA in the range of 1,000 bp to 5,000 bp, we must be explicitly notified of the request. Failure to do so may result in an additional charge to run the appropriate assay for DNA of this length.
    • * For DNA >5,000 bp, please see High Molecular Weight DNA QC guidelines below.
  • Sample volume of 10-50 µl with a concentration no greater than 50 ng/µl.
    • Providing <5 µl may result in our ability to perform both assays.
    • Samples >50 ng/µl will result in dilution in order to properly perform the assays.
    • Residual sample will be disposed.

High Molecular Weight DNA QC (NanoDrop, quantification, size analysis with Femto Pulse)

  • Follow ALL General Guidelines above.
  • This service provides purity assessment, fluorometric quantification, and size analysis of dsDNA.
    • While certain fluorometric and size analysis assays are capable of quantification/detection of ssDNA, the assays we perform are intended for dsDNA.
    • Size analysis can only be performed after quantification.
  • If you intend to have additional services performed on your DNA or libraries after QC, please see the appropriate Guidelines for Submitting DNA for Library Preparation or Already Prepared Libraries.
  • Genomic DNA or high molecular weight DNA is the intended input, but any DNA in the range of 1.3 kb to 165 kb is acceptable.
  • Sample volume of 10-50 µl.
    • Providing <5 µl may result in our inability to perform all assays.
    • Residual sample will be disposed unless an explicit request is made for return.

DNA Shearing (Covaris M220 focused-ultrasonication)

  • Follow ALL General Guidelines above.
  • This service provides shearing of gDNA through focused-ultrasonication with Covaris M220 using microTUBE-50. Validated protocols can be run to obtain mean fragment sizes of 150, 200, 250, 300, 350, 400, and 550 bp. More information on protocols can be found from the manufacturer.
    • DNA shearing includes quantification prior to shearing and size analysis after shearing.
  • Sample volume of 50-55 µl.
  • Up to 5 µg of DNA at a concentration of <100 ng/µl.
  • Manufacturer recommends Tris-EDTA, pH 8.0. Other buffers may be suitable for your application.
  • Length of gDNA should be >10kb.

DNA Size Selection (PippinHT or BluePippin)

  • Follow ALL General Guidelines above.

PCR and Other DNA Cleanup (SPRI bead Cleanup and Size Selection)

  • Follow ALL General Guidelines above.

High- and Low-Throughput Fluormetric Quantification

  • Follow ALL General Guidelines above.
  • This service provides fluorometric quantification of dsDNA.
    • While certain fluorometric assays are capable of quantification of ssDNA, the assays we perform are intended for dsDNA.
  • Sample volume of 10-50 µl.
    • Providing <5 µl may result in our inability to properly perform the assay.
    • Residual sample will be disposed unless an explicit request is made for return.