Submission guide for samples in 96-well plates

The most efficient way to run 16 capillary sequencers is to make sure each run is maximized, or contains 16 samples. For every run, regardless of the number of samples, the sequencer fills the 16 capillary array with fresh polymer for the samples to electrophoreses through. Therefore, in an effort to prevent the waste of polymer and machine time please follow these guidelines. More sample submission information can be found here.

1. Organization of a run on a 96-well plate.

ABI Genetic Analyzers are automated capillary electrophoresis systems that can separate, detect, and analyze up to 16 capillaries of of fluorescent labeled DNA fragments in one run. One run is defined as, at most, 16 sample wells, a 96-well plate can be divided into 6 runs. This is shown in figure 1.

2. Organizing samples on a new plate.

User must submit samples in multiples of 16, or more than 48 samples at one time. In any case, you should load your samples starting from column 1,3,5,7,9 or 11.

3. Organizing your samples on a partially used plate.

The sequencer is capable of performing a run at any place on a plate as specified by the users. This allows users to partially load and run a plate on one date, then finish loading and running the plate on another date. The following example is designed to help understand how the Core lab would like this to be approached.

Say that the first time that you load and submit a plate to be sequenced you have 56 samples, which uses all of columns 1-7 and would constitute 4 runs on the array (figure 2).

After the runs on this plate are completed there are 40 empty wells in 5 columns. If you wanted to use the empty wells to run 16 samples, you would want to use rows 9 and 10 and not rows 8 and 9. In using rows 8 and 9, the sequencer would have to perform two runs to compile sequence for all 16 samples (figure 3).

The way the software and the 16-capillary array interact is that each 16 sample run must be added to columns 1 & 2, 3 & 4, 5 & 6, 7 & 8, 9 & 10, or 11 & 12. Sequencing 16 samples added in any other configuration will result in the sequencer performing multiple runs. Therefore, the most efficient way to add 16 samples to this plate would be filling columns 9 and 10 (figure 4).

By following these suggestions the Core lab will be able to process samples in a more timely manner and reduce the cost of the general operation of sequencing and fragment analysis. More sample submission information can be found here. Thanks, and happy cycle sequencing.