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Probes with similar subcluster specificity, were further ranked using the Nimblegen ranking algorithm, which accounts for uniqueness, distribution within the sequence (aimed at an even distribution), and probe manufacturing parameters.
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These finished libraries were enriched using the Nimblegen SeqCap kit.
Microarray was carried out using the NimbleGen microarray service.
Images were extracted and processed using NimbleScan v2.4 software and analyzed using the NimbleGen commercial pipeline.
cDNA was labeled using the NimbleGen Dual-Color Labeling Kit (NimbleGen) according to manufacturer's protocol.
The probes were designed and printed by Nimblegen using the Nimblegen probe design pipeline previously published (Roche Nimblegen Probe design Fundaments 2008).
After incubation, arrays were washed using the NimbleGen Wash Buffer Kit and dried using the NimbleGen Slide Dryer.
500 1000 ng of isolated DNA was labeled using the NimbleGen Dual-Color Labeling Kit (NimbleGen) according to manufacturer's protocol.
Double-stranded cDNA was cleaned and labeled using the NimbleGen genes expression analysis protocol (NimbleGen Systems, Madison, WI, USA).
DNA (500 ng) was labeled with either Cy5 or Cy3 using the NimbleGen Dual-Color DNA Labeling Kit (NimbleGen).
Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA).
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