"Transcriptomics & Functional Genomics"

"Update on droplet digital PCR"

Bio-Rads QX100 droplet digital PCR instrument

Some of you may be aware EUC recently supported the funding and purchase of a Droplet Digital PCR (ddPCR) instrument jointly by two groups in Clinical Sciences. This instrument, the Bio-Rad QX100 was commissioned in January 2013 and is housed in room 2.107 in Medical Biomics on level 2. The instrument enables the creation and reading of PCR emulsions allowing digital PCR to be performed. The PCR component of ddPCR is carried out in a standard PCR instrument compatible with the plastics used by the droplet reader. The QX100 has advanced capability covering standard TaqMan chemistry compatible with FAM and VIC/HEX probes, it can therefore perform duplex PCR.

Training on the instrument is being provided on request on a personalised adhoc basis as appropriate to the users needs, you are encouraged to contact Dr K Laing.


How do I access the QX100 and what are the charges

  • No charge currently will be made for access to this instrument. However, electronic access to the room 2.058 on corridor 3a requires card access activation, in which case to access the room you need to fill out the access form you can down load it from here. Authorisation can be provided by Dr Ken Laing..
  • Prior training and approval on the use of the instrument is a requirement for access. This can be obtained by contacting Dr K Laing klaing@sgul.ac.uk.
  • Advanced Booking should be made. The time and duration you wish to use the instrument in advance, giving your full name and contact details. This can be done on-line using a Convergence calendar
  • More information will become available on-line click here

How do I Book on-line using a Convergence calendar

  1. open convergence and login with your medical school login, search for “QX100” calendar by selecting the “create or subscribe” icon on the upper left, just above “my calendars”
  1. select “subscribe to calendar” in the drop down box, the main window will provide new tabbed window with a search box. Type in “QX100” and click search.
  2. As owner of the Calendar my name (Ken Laing) will appear below click on it and the QX100 calendar will appear on the right, click on the Calendar and then the subscribe button on the bottom right. You should have both read and write permission to this Calendar

What reagents and consumables does the instrument require

The instrument is only compatible with Taqman or similar probe based chemistries and including FAM and VIC/HEX probes (it is NOT compatible with Sybr green or hybridisation probes like molecular beacons). Plastic consumables should be from the sources listed below however, these are standard profile type plates but it is imperative that plates and foil seals used in the QX100 are those listed; the retail price of this instrument is around £60K and damage to it through incorrect useage is therefore a serious matter. See below:

  1. Reagents

      The creation of a uniform emulsion with droplets of a specific size and uniformity is critical to the performance of the system, as a consequence standard reagents are not compatible with the instrument and will lead to problems. Currently only reagents specifically designed for the instrument supplied by Bio-Rad can be used, this may change in the future.

      The instrument is calibrated on FAM, VIC and HEX.

      • 2X ddPCR supermix for probes, includes 5, 1mL tubes BioRad cat# 1863010
      • Droplet generation oil, includes 10, 7mL bottles BioRad Cat# 1863005
      • 2X Buffer Control Kit, includes 2, 4.5mL bottle (this is only used to fill cartridge wells that do not contain sample) BioRad Cat# 1863052
  2. Plastics

      Consumable plastics for the droplet generation and gaskettes are only available from BioRad, however seals and plates are also avaiable from elsewhere see below:

        Bio Rad

      • DG8 Cartridges, 24 cartridges, 1pkg BioRad cat# 1863008
      • DG8 Gaskets, 24 gaskets, 1pkg BioRad cat# 1863009
      • Hard-Shell High-Profile 96-well semi-skirted PCR plates, green shell, clear well 25 plates BioRad cat# HSS-9641
      • Easy piercable foil heat seal, 100 seals BioRad cat# 181-4040

        Eppendorf and Thermo Scientific (ABgene) available through Fisher

      • Twin Tec semi-skirted 96-well plate Eppendorf cat# 951020362
      • Easy Pierce Foil PCR Plate Seals Thermo cat# AB-0757

      For current pricing either contact the company reps or ask for more information

What Chemistries can I use

  • The QX100 is only compatible with TaqMan style probes (FAM, VIC/HEX) and real time PCR applications

What software is available to analyse my data locally

We currently running software version on Windows 7. This software can be used locally to open your run-files, perform common methodologies for analysis setting manual thresholds combining wells along with absolute quantitation, rare event detection and copy number variation analysis.

More information generally about Real-time PCR and droplet digital PCR

  • More detailed support and advice for this and other Real-time instruments can be obtained by contacting me Ken Laing klaing@sgul.ac.uk
  • For more general information see my own web pages at http://www.ipc.nxgenomics.org/newsletter.htm and http://www.ipc.nxgenomics.org/
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