PacBio Sequencing

The UO GC3F now offers Pacific Biosciences (PacBio) sequencing services on our newly installed PacBio Sequel system!  Single Molecules of native DNA are sequenced in Real Time on the Sequel instrument utilizing devices called "SMRT cells".  Each SMRT cell can yield between 5 and 10 Gb of sequence data, with a read length of greater than 10 kb on average.  

Curious about how this works?  Watch this.

 

Pricing:

Sample Preparation *  
Internal Rate (per library) $450.00
External Rate (per library) $675.00
Sequencing  
Internal Rate (per SMRT cell) $800.00
External Rate (per SMRT cell) $1,200.00

CLICK HERE to submit request for PacBio sample prep or PacBio sequencing! (Note, you will need to register for an iLab account.)

 

*Obtaining sufficient quantities of high molecular weight DNA for PacBio sample preparation can be difficult.  Additional service fees (Fragment Analyzer, Pippin Prep, etc.) may apply for extra QC and troubleshooting.

*Please also note that the amount of final library obtained from PacBio preps is highly variable (depending on DNA quality, fragment length desired, etc.). If you are planning to sequence a large number of SMRT cells, we may need to scale up the library prep in order to obtain enough library, which would increase the prep cost accordingly. For example, if we needed to scale up the reaction by a factor of 4 to generate enough library to sequence on 36 SMRT cells, that would increase the prep cost by a factor of 4 (so $1800 instead of $450 for internal pricing). If you have a specific scenario in mind, please contact us to discuss options.

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IMPORTANT NOTE FOR USER-PREPPED LIBRARIES:

If you are planning to prep your own PacBio libraries, please be sure to ship them frozen on dry ice in a well-padded vessel to protect the tubes. Jostling of thawed samples during shipping may damage your libraries and prevent sequencing. 

To submit a completed library for sequencing, please register for an iLab account and then click "Request Services" from the top menu bar in iLab. It is important that your sequencing request has been submitted in iLab before you provide the physical samples to us!

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IMPORTANT NOTES FOR GC3F-PREPPED LIBRARIES:

If you are planning to provide the GC3F with DNA for us to make the PacBio libraries for you, the quality of the input DNA is extremely critical for ensuring adequate library yield and high sequencing quality. Please be sure your purified dsDNA meets the following strict PacBio requirements:

  • All steps of DNA extraction, purification, and storage performed in Eppendorf LoBind tubes
  • Submit a minimum of 5 µg dsDNA (ssDNA cannot be prepped)
    • Must be quantified using a fluorometric assay such as Qubit or Quant-iT (spectrophotometric assays are not adequate)
    • Be sure to very thoroughly (but very gently!) mix your sample using wide-bore tips prior to taking an aliquot for quantification
    • If you have less than 5 µg, please contact us to discuss options
  • DNA is of high quality = 
    • Fragments are of sufficient length for your desired sequencing application (contact us for details on your specific project)
    • No RNA present
    • Has not been exposed to intercalating dyes, UV radiation, ethidium bromide, high temperatures, extreme pHs, or vortexing
    • Minimal nicks, breaks, and other damage
    • Minimal time spent stored at 4°C
    • Minimal freeze-thaw cycles (also allow sample to fully thaw before any mixing, as ice chunks can shear the DNA)
    • If shipping to our facility, must be sent frozen on dry ice in a well-padded vessel to protect the tubes
  • DNA is highly purified =
    • Purified and stored in EB or TE buffer
    • 260/280 nanodrop ratio = at least 1.8
    • 260/230 nanodrop ratio = between 2.0 and 2.2
    • No visible particulates, precipitates, colors, cloudiness, or viscous substances

To submit dsDNA for library prep service, please register for an iLab account and then click "Request Services" from the top menu bar in iLab. It is important that your Sample Prep request has been submitted in iLab before you provide the physical samples to us!

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Please contact Doug Turnbull or Maggie Weitzman for further details on PacBio sample submission. Thank you!