Illumina has recently discovered that use of ammonia-based cleaners or sanitizing products near sequencing run setup (lab benches, pipettes, etc.) can result in decreased sequencing run performance metrics. 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 (on nonpatterned flow cells), variable percent clusters passing filter (for both patterned and nonpatterned flow cells), or lower than expected starting intensities on your sequencing runs, make sure that ammonia-based cleaners are not used 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 used, Illumina recommends: