Choosing the right slide for spotting microarrays is much like picking the right film to commemorate a cherished vacation. Just like the photographer who needs the right speed to capture the bright light on the beach or on the mountaintop, or catch the twilight between the ruins, researchers want the right slide to give them the lowest background and best signal-to-noise ratio with their preferred experimental protocols.
With a growing number of companies catering to the needs of self-spotters, fewer and fewer microarray facilities coat their own slides. But the choice can be difficult, and not every brand lives up to its promises. BioArray News surveyed about 20 users, most of them at academic microarray core facilities, about the slides they prefer and what is most important to them. The wish-lists were consistent: the ideal slide for a particular application – be it cDNA, oligo, or protein printing – should offer a low and homogeneous background, a high signal-to-noise ratio, consistent spot morphology, no lot-to-lot variability, good hybridization, compatibility with different buffers and experimental conditions, and all that at a reasonable price – an important factor especially for academic facilities.
Slide prices, in fact, vary widely, depending on the brand and type of coating. Most providers offer discounts on large quantities, making price comparisons difficult.
Most of the users have undertaken some effort to find the slide that suits their needs best: three-quarters mentioned they had compared several brands, and half of those said they were still testing new slides coming to market, especially to find a cheaper option. Like settling for a brand of film that once captured a beautiful sunset, many users stick to their choice once they are satisfied with the results. A fair comparison is hard to make because companies recommend their slides for specific applications, and prescribe certain buffers for optimal results. Moreover, labs use different protocols for blocking, labeling, and hybridization.
However, certain trends emerged from the survey: Seven users said they found Corning’s GAPS slides best for arraying cDNAs and oligos and are using them routinely now, despite a steep price of more than $10 per slide. Three users said they have had good experience with various Cel Associates products, also distributed by TeleChem International, pointing out their reasonable quality for a rock-bottom price of less than $2 per slide. Telechem’s own SuperAmine is the slide of choice for two institutions, and another two use Asper Biotech’s SAL slides. BD Biosciences Clontech, Bioslide and Quantifoil each received one mention as the preferred brand.
Four academic facilities, however, are still betting on homemade poly-L-lysine slides, even after testing a variety of commercial products. Although some said they would be happy to switch to a commercial provider in the future to avoid the time-consuming coating process, no product currently beats their “homebrews” in terms of quality and price. One facility even went back to coating its own slides after a manufacturing problem with their commercial provider affected their experiments for three months.