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  • Ion Chef

    Hello,
    Has anyone had their Ion Chef installed yet? Do you always have to prepare two chips at a time? I've been reading through the instructions and it seems to rely on you having two Sequencers to run the chips on. It does say chips can be stored for 4.5 hours but a sequencing run is longer than 5 hours so it looks like you can't run the second chip!

  • #2
    The v3 chemistry only takes a bit over an hour to run.

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    • #3
      what read length? PE?

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      • #4
        200 SE, the new Ion High-QT will be 400 SE

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        • #5
          So, let me get this straight: you are saying Ion's new sequencing chemistry will be sequencing SE 200 and 400 bp in 1 hour sequencing runs. Is that correct?

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          • #6
            Originally posted by MrGuy View Post
            So, let me get this straight: you are saying Ion's new sequencing chemistry will be sequencing SE 200 and 400 bp in 1 hour sequencing runs. Is that correct?
            No, that is not what he meant. The Ion Chef is Life Techs new sample prep machine for automated library and size selection. The 1 hour is for the library amp step, instead f the 5 hour step now.

            The sequencing will still take the 4-5 hours.

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            • #7
              ok, so it's:
              OT2+ES+chip loading --- 5-8 hours
              Isothermal+ES+chip loading -- 2 hours
              Chef -- 10 hours for two chips
              Sequencing still at 4 hours

              In other words, with Chef, 18-20 hours would produce two 200 or 400 bp SE runs on one sequencer or ~15 hours for two sequencers

              Or with IsoChef (if that is for real) then as little as 6 hours for two runs with two machines. That's a regular work shift.

              Extrapolate on that...
              DNA extraction - 30 min
              Exome Ampliseq 2 hrs??
              Lunch 2 hours :-)
              IsoChef -- 2 hours
              200 bp run -- 3hrs??
              Autoanalysis on torrent server

              Exome in a day. That's crazy. Wonder if they will really ever get there.

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              • #8
                Close, I think you just have your terms jumbled.

                workflow now:
                extract-->OT2+ES+Chipload-->PGM/ION --->
                30min --> 5-7hours --> 4ish hrs extraction and sequecning one chip in a day

                Workflow early adaptors: still one chip in a day
                extract --> Isolthermal+ES+chip loading ---> PGM/ION
                30min ---> 2hours ----> 4ish hrs

                Workflow with Chef:two chips in a day
                extract ---> IonChef ---> PGM
                30-60 min 2hrs 4ish hrs

                The chef is suppose to be the isothermal+ES+Chipload all in one hands free device.

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                • #9
                  Hi,

                  Has anyone tested out Ion Chef? If so, what are your thoughts on it?

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                  • #10
                    We get improved loading and more uniform results.

                    Our biggest issue is consistent quantification of libraries for emulsion PCR.

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                    • #11
                      What do you use to quantify your library for emulsion PCR?

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                      • #12
                        We use the Nanodrop and/or the Bioanalyzer to normalize to a library which gave good sequencing results.

                        This works for the most part. We used to use QPCR but the adaptors we are using don't work with the LifeTech QPCR probe.

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                        • #13
                          In case you are looking to try something else, we use Qubit fluorometer and dsDNA High Sensitivity reagents. It is really quick assay and our experience has been great! I would definitely recommend over the Nanodrop.

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                          • #14
                            Originally posted by madebeljak View Post
                            In case you are looking to try something else, we use Qubit fluorometer and dsDNA High Sensitivity reagents. It is really quick assay and our experience has been great! I would definitely recommend over the Nanodrop.
                            Same here, Nanodrop can be off by 50%, Qubit never is.

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