Hi everyone, not especifically a BioC question this time... but I am hoping to use the collective experience regarding a particular array design. We're considering using human expression arrays from Nimblegen. Essentially, we're not sure which format to go for: 1) 6-20 60-mers per target 2) 2-7 60-mers per target The design #2 uses less probes per target, allowing to have 4 times a 72k array on one slide (which can be hybridised with separate samples), rather than 1 time a 385k array. So it's a smaller array but being able to hyb 4 samples in one array reduces costs quite a bit... so it's attractive, and my feeling is that it shouldn't be too problematic to reduce teh number of probes per gene to this level... but it's just a "feeling", having little experience on this type of arrays. Any thoughts about this? Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

Hello, my feeling and previous experience is that, with 60mers, you can get reasonable estimates for transcript concentration from a few probes only, as long as the 60mers are sufficiently specific for that transcript and distributed all over the array platform and not next to each other. In fact, Illumina uses one single 50mer per transcript for their beadarrays, but that one in about 30 copies all over the array to the effect that you get a very precise measurement for that oligo. In your case, you probably want to be sure that the 60mers are specific for the genes/transcripts, have comparable GC contents, and no (partial) matches to other genes. See the paper by Rennie, Hoyle et al. in BMC Genomics for a recent, good paper on the effect of mismatches in long oligos. The development version of Biostrings provides good, fast tools for assessing (partial) reporter matches in a genome. Nimblegen probably does a good job with the probe selection, but if you conduct such an assessment yourself beforehand, you will know what kind of cross-hybridization you could expect to see later in your data. Regards, Joern J.delasHeras at ed.ac.uk wrote: > > Hi everyone, > > not especifically a BioC question this time... but I am hoping to use > the collective experience regarding a particular array design. > > We're considering using human expression arrays from Nimblegen. > Essentially, we're not sure which format to go for: > > 1) 6-20 60-mers per target > 2) 2-7 60-mers per target > > The design #2 uses less probes per target, allowing to have 4 times a > 72k array on one slide (which can be hybridised with separate > samples), rather than 1 time a 385k array. So it's a smaller array but > being able to hyb 4 samples in one array reduces costs quite a bit... > so it's attractive, and my feeling is that it shouldn't be too > problematic to reduce teh number of probes per gene to this level... > but it's just a "feeling", having little experience on this type of > arrays. > > Any thoughts about this? > > Jose > -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk