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Old 12-02-2016, 06:47 AM   #9
Location: Brazil

Join Date: Aug 2015
Posts: 69


Originally Posted by lucorum View Post
r.rosati, about OT2:
I tried to download the logs right after the run, so the instrument was continuosly turned on and shouldn't lose data. I formatted two different flash drives in FAT32 (FAT32 is a default file system for these drives, and it wasn't specified in the protocol what file system it must be) and tried to write logs on each of the drives at least twice, and failed. I will try FAT next time, thank you for advice.
FAT32 is OK, so unfortunately this is not the problem.

Originally Posted by lucorum View Post
Our OT2 instrument isn't connected to the server and I don't know how to connect it (I think it should be quite simple, though).
Oh. Are you updating it via USB? So does your OneTouch2 recognize the USB for installling updates?

Originally Posted by lucorum View Post
I also have another (stupid) question about used chips: we recently purchased some new, v3 chips, and still didn't use one, all our used chips are v2. Would it be OK to use old v2 chips for cleaning and initialization and then v3 chip for sequencing?
Yes you can still use them for cleaning; about initialization, yes, but it depends on how old they are.

Notice that v2 and v3 chips are "indistinguishable" by our Ion Proton (they're both identified as the same version); the difference between them is that the new v3 one is prepared (but expires), the other needs prep (but doesn't expire).

So you can also still use new v2 chips for sequencing. This is how I do it, but mind, the "usual" prep might perhaps be enough:

Originally Posted by r.rosati (on IonCommunity)
We used a simple system to ease the preparation process. We used a "third hand" grip (as for electronics work) to keep a vacuum line in place within the exit well of the chip, near but not above the exit port (to prevent aspiration of liquid from inside the chip). This streamlines the washing procedure and allows for using 1ml syringes to clean the chip.

So basically the difference is that whenever the protocol called for injecting 200 ul, or 2x 200 ul of isopropanol/water/NaOH, we would just inject a whole 1ml.

The preparation protocol was thus:

1) Three cycles of:

- inject 1ml isopropanol

- vacuum dry

- inject 100 ul of chip preparation solution, remove the excess

- incubate 2 mins, 50C

- inject 1ml isopropanol

- inject 1ml water

- inject 1ml NaOH

- Incubate 1 min, RT

- inject 1ml water

(so it's basically the same back-and-forth of: chip prep, iPrOH, water, NaOH, water, iPrOH, chip prep - just with 1ml and automatic vacuuming of the solutions at the exit well.)

2) Inject 1 ml isopropanol

3) wash the loading well with 100 ul isopropanol

4) vacuum-dry

5) store at RT, in a dry container away from light, until the next day

The chips were used the next day, directly as stored. The ISPs are added to the dry chip, and then we followed the Hi-Q protocol by the book. This means that there is no need to calibrate the chip before the run, because empirically, the pre-run calibration of the Hi-Q program is equivalent to the pre-run calibration step in the v2 chip protocol.

Last edited by r.rosati; 12-02-2016 at 06:54 AM.
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