Up Close and Personal With the Ion Chef System

Working at a place like Thermo Fisher means that there are many people working on many projects simultaneously. On a recent visit to the Systems Engineering group, we found them making sure the Ion Chef™ System for automated template prep integrates well from both an engineering perspective (think hardware and the software that controls it) and a biochemistry perspective (think percentage of wells on the sequencing chip that are producing data).

As seen in the first photo, towards the left side of the system, there is a foil-covered amplification plate where the Ion Sphere™ Particles (ISPs) are amplified after thermal cycling. To the right of this area are two centrifuges used for the breaking process. The white sleeved inserts (with one removed and laying on the surface of the enrichment area) are used, six per sample, to collect the amplified ISPs. Between the amplification plate and these centrifuges is the enrichment area (the white strip with eight individual tubes). A motorized magnet rises below the deck surface during the magnetic bead-based enrichment process. After automated enrichment comes automated loading of beads onto the chip.

In the photo, the chip centrifuge is in front of the amplification plate (with a rotor cover resting on top of the lid). On the rotor cover, you can see three silicon-like rings that provide a pipette-tip-pierceable air seal to assist with loading of the enriched ISPs onto the chips (the Ion Chef™ system can handle up to two chips per run). A chip bucket is resting to the side of this centrifuge. The white gasket adapters on top form a second barrier around the pipette tip and assist with alignment

The second photo shows Brittany from System Engineering holding a chip centrifuge bucket and pointing out the bucket’s unidirectionality. You can only insert the bucket one way, since it is weighted to ensure a 90° orientation when centrifuging. This was accomplished by designing one of the bucket arms to be larger and longer than the other (the one under her thumb is visibly shorter).

In the third photo you can see the different orientations within the bucket for the Ion PGM™ 3-series chips compared to the Ion Proton™ PI chips. The same centrifuge bucket design is used for both chip types, but the 3-series chip is oriented at a 45° angle, while the PI chip is oriented straight-on. Note the 2D barcode that the laser vision system detects as part of its startup routine to positively identify the particular chip used for a given run.

In the last photo Brittany shows the white gasket adapter for the Ion PGM™ 3-series chips, which provides the important interface between the pipette tip and the chip during the bead-loading process. The Ion PI™ chips have a different adapter that serves the same purpose.

Learn more about Ion Chef™ automated template prep system. And if you have a few minutes, check out this video about Ion Chef automated library template preparation.