Origin of image artifacts. Correct instrument adjustment is an important prerequisite for producing high quality sequencing data. Preparation and start of a sequencing run has to be done with careful attention to avoid or identify the following instrumentation artifacts: (A) Air bubbles, caused by leaks, insufficient priming of reagent pumps and long waiting times. Bubbles can obscure parts of the images or reduce chemistry efficiency. (B) Particles in the sequencing chemistry (e.g. crystals from an unfiltered incorporation mix) frequently result in image artifacts. (C) Incorrect adjustment of stage flatness and stage tilt can cause distortions, i.e. parts of the image are sharp while the rest is out of focus. A similar effect limited to tiles at the flow cell edges, can originate from liquids covering the flow cell surface. (D) Reflections in the GA instrument can cause variation in cluster brightness, like the commonly observed band of bright clusters in column 2 of lane 8. (E) If the position of laser excitement is not in sync with imaging (footprint) on GA instrument, a black straight band can be observed at the edges of multiple tiles (partially with comb like slots). (F) If this effect is limited to tiles at the flow cell edges, oil coverage is insufficient.
Kircher et al. BMC Genomics 2011 12:382 doi:10.1186/1471-2164-12-382