Table 3 Troubleshooting Guide

Genome is not fragmented after sonication.

Buffer condition is not adaptable for sonication.

Purify the DNA. We used QIAGEN PCR Purification Kit, eluted in EB to have it work.

Nothing is visible on the gel after 1 hr electrophoresis during library generation.

When the starting amount of DNA is small or there is significant DNA loss during the process for various reasons, it is possible that the DNA is smeared over a wide range after an hour of electrophoresis and not visible on the gel.

It is good to check the gel to see if the DNA is present after ~10 min run when the DNA is not smeared at a wide range.

Even though nothing is visible, it is highly possible that the DNA is still present. Proceed to the next step regardless and see if PCR amplifies anything.

Cannot collect ~400 ul after the stripping step.

Gasket slide was re-used.

The array slide was lifted up too quickly.

Different buffer was used for the 95C stripping process.

Do not re-use the gasket slide.

The solution can be flushed to a collection boat and collected.

When using multi-array slides like 2×105 K, 4×44 K or 8×15 K, it is still possible to run the capture protocol as indicated. After the stripping, the array slide should be slowly lifted up to prevent contamination. The solution tends to stay within the gaskets.

Not enough DNA amplified after the first stripping.

Stripping was not efficient.

Another stripping process can be done and checked if there were left over genomic fragments hybridized on the probes. Since it does not matter if the stripped solution contains contaminants as long as the contaminants do not have adapters ligated at the end, it is possible to thoroughly continue the stripping process until no products get amplified.