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Back to Protocols

Machines available as of 7/2013

Thermocycler location Appearance Brand Capabilities/Quirks Manual Use restrictions*
Janet's bench black DNA Engine: DYAD small block doesn't do gradient; large block does NA none
Janet's bench white BioRad: C1000 Touch:185-1148 2 gradient blocks, 48 wells each C1000 none
Amanda's window white & new Eppendorf: Mastercycler gradient gradient (left --> right), but see manual b/c it is weird Mastercycler Gradient none
Frances' window black & old DNA engine no gradient n/a none
Nate's Bench white, smaller Eppendorf: ?? no gradient ## none?
Alexey's Bench old beige BioRad: S1000 2 gradient blocks. Gradient = front to back. 50uL max S1000 none
Ceci's window white, small Eppendorf: ?? no gradient ?? (see note 2 below)
Marina's Bench black ?? real-time PCR (see note 3 below) ?? (see note 1 below)

Note 1: All PCR system in the lab are public, but coordination of use helps

Note 2: "I would like to be informed if anyone is planning to use it, as this summer we will use it heavily. But everybody is welcome to use the machine in my bench as long as people let me know so I can plan accordingly." - Ceci 6/2013

Note 3: for RNA quantification. Could do regular gradient PCR if needed, but is usually only used for RNA.

Specific Tips for Individual Machines

Biorad S1000

  • Folders are possible.
  • To save a protocol, scroll to the bottom and press cancel. It will ask you whether or not you want to save.
  • Using a gradient:
    • You set two numbers for the boundary temperatures.
    • Setup the gradient inside a protocol. You can't view the position temperatures from this interface.
    • To view a gradient:
      • Start the protocol with the gradient you entered, and promptly quit the protocol. Then press the "Screen" button on the left.
  • Closing the lid:
    • The door action is very unusual. Press back, then lower the arm. Twist the cap until a tiny amount of resistance is felt, then tighten about a quarter turn. It is easy to crush your tubes.

What makes for a good thermocycler?


  • gradient block(s)
  • multiple blocks on one machine
    • reduces the need to enter programs into many machines
  • allow for saving of protocols in folders
    • different researchers can have different folders, preventing the accumulation of a huge list of protocols, and others accidentally writing over other peoples' protocols
  • large maximum volume per tube (100 uL is common)
    • Good for building purification-scale quantities of product.
  • quiet heating & cooling
    • It is very distracting to have a noisy thermocycler right next to your head while you need to do focused thinking!


  • intuitive menu hierarchy
    • NOT true of eppendorf systems!
    • BioRad system is fantastic
  • Show what happens to each well for a given gradient setting *while* the protocol is being edited
    • Not true of white eppendorf Mastercycler gradient

Bonus Points

  • ability to recall past thermocycling programs used
    • occasionally useful for troubleshooting failed reactions
  • Optional mode that shows how long until a protocol is compete
    • Marina's BioRad system's screen goes black with big light up numbers indicating how long until it is complete. It can be seen from several benches away. (This machine is no longer here.)