Why Run Timing Matters
In a multi-condition microfluidic experiment, carryover is invisible until it ruins your data. If you start collecting fraction 2A one minute too early, it contains residual condition 1 fluid. At qPCR sensitivity, that is indistinguishable from a real signal.
The fix is a well-specified flush protocol: wait long enough for the new sample to fully displace the old one before collecting anything. The minimum wait is the system dead volume divided by the flow rate, multiplied by a safety factor (2× for routine, 3× for quantitative, 5× for sticky).
Writing this schedule on a scrap of paper at the bench invites transcription errors. A printable timeline with absolute clock times is the cheapest possible fix.
Planning Your Fractions
Fraction volume is a tradeoff: larger fractions give you more material per sample but fewer time points; smaller fractions give you better temporal resolution but less material per sample and more tubes to label.
For routine collection, 50–200 μL fractions work for most downstream assays. For gradient-based separations or time-resolved experiments, drop to 20 μL and expect to fill a 96-well plate per condition.
The scheduler drops any fraction that would overflow the reservoir after the flush — no partial tubes.
Run-Day Checklist
Before you start the pump:
1. Load reservoirs for every condition and label them
2. Label collection tubes ahead of time (tube 1.A, 1.B, … 2.A, …)
3. Verify your flow rate on the pump display
4. Start the pump at the scheduled start time
5. Set a kitchen timer for each event from the printout
The scheduler is a plan, not a controller. The timestamps depend on you following the plan.
