High-throughput oligo synthesis Agilent vs. Nimblegen

[jffkm]

Hey guys, I've been following George Church and Shendure's work and had a general question regarding optimal cost-feasibility for synthesizing a lot of oligos.

The next round of experiments we plan will require on the order of 1 million primers so we are considering array based methods as cost or normal synthesis will be prohibitive. Shendure uses agilent arrays that he strips the oligos off of but I have heard from nimblegen representatives that using strong NaOH washes on their custom arrays also strips their probes off to a "certain degree." can anyone confirm successful design and recovery of sufficient oligo [] from a nimblegen array for PCR? This is not a traditional hyb-elute strategy but it would be a non-traditional use of a nimblegen array. They are much cheaper than agilent options so we'd like to go this route if possible. Please let me know if you get a chance. Thanks!

[chenbati]

why NimbleGen option is much cheaper than Agilent option?

Agilent is actually offering custom library of oligos cleaved from the array slide. Does that fit your purpose?

[samanta]

Nimblegen option could be cheaper, because their arrays have much higher density than Agilent arrays. I am saying this only from my familiarity with their respective array technologies.

[Jon_Keats]

Remember you often get what you pay for (ie. its cheaper for a reason). In regards to eluting off the arrays, we often strip and reuse agilent CGH arrays multiple times with little effect on signal intensity so I doubt we are cleaving off the probe.