Hi everyone! I was trying to figure out what was the cheapest and fastest extraction method to automate RNA extraction on an Opentrons liquid handling platform and I ended up with a quite long list of suppliers and prices. You can find it at this link:
The first page shows the estimated costs for:
- RNA purification using magnetic beads
- RNA purification using silica columns (Jena bioscience kit)
- RNA purification using silica 96 well silica plates + Quiagen Buffers
- RNA purification using silica 96 well plates + Macherel Nagel Buffers
- RNA purification using 96 well silica plates and homemade reagents
The “time” row refers to running a simulation of the automated protocol on an Opentrons platform.
For each method I tried to pick the cheapest reagents I could find and a list (I tried to tidy it up, but it may still look messy) is available on the second sheet of the .xls file, with an estimated cost per sample and link for the supplier.
Feel free to provide feedback if you know cheaper suppliers or have tried any of those methods!
Find here a summary of the three main methods:
| Method | Estimated cost per sample | Estimated processing time with Opentrons | pros | cons |
|---|---|---|---|---|
| Magnetic beads | 0.87 £ | h 15 min (for 96 samples) | -cheapest method -high thoughput -fully automated | - slow -requires validation -requires optimization |
| Silica column kit | 1.77 £ | 1 h (for 24 samples) ~ 3h 30 min (for 96 samples) | -validated -faster washing steps compared to beads | -semi-automated -expensive -slow |
| Silica 96 well plates + Quiagen Buffers | 1.11 £ | 50 min (for 96 samples) ~ 3h (for 384 samples) | -fastest method -high throughput -similar to columns (same buffers) | -requires validation of the plates -more expensive than beads |