Illumina has recently discovered that use of ammonia-based cleaners or sanitizing products in proximity to sequencing run setup (lab benches, pipettes, etc.) can result in decreased sequencing run performance metrics. Metrics, including decreased or variable cluster densities and low starting intensities, have been seen by customers.
The mechanism by which this effect occurs may be linked to the effect of ammonia on DNA structure (Zinchenko et al 2004).
If you are experiencing variable cluster density, variable percent clusters passing filter (on patterned flow cells), or lower than expected starting intensities on your sequencing runs, ensure that ammonia-based cleaners are not in use in the lab environment. Inspect ingredient lists of cleaners or antibacterial wipes for ammonia or quaternary ammonium compounds such as benzalkonium chloride (alkyldimethylbenzylammonium chloride) and dialkyldimethylammonium chloride.
If ammonia-based cleaners have been in use, Illumina recommends: