DNA library shoulder peak on bioanalyzer

[krabidou]

Hi Everyone,

We recently just processed a few DNA libraries using the Illumina Truseq PCR free kit. When we ran them on Bioanalyzer, one of the libraries came out perfect, with a single peak centered around 500 bp. The others, however, have a secondary shoulder peak ( ~ 375 bp) attached to the main library curve. We have never had this happen to our previous libraries. Has anyone else seen this/know the underlying cause and how to avoid it? Thanks!

[nucacidhunter]

Few points:

1- Chip is overloaded
2- If shoulder is not consistent among the samples it could be due to vibration during Chip run.
3- Is the perfect library concentration is lower than the others. If true it would indicate artefact of overloading Chip.
4- The trace is not similar to TruSeq PCR-free library profiles (350 or 550 bp insert)
5- If shoulder is real, could be the result of size selection step