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The procedures have evolved through 6 years of operation and have resulted in at least 50 publications acknowledging the use of microarray slides and/or services provided by the Resource.
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We acquired fluorescent images of microarray slides using a ScanArray confocal laser microarray scanner (Packard BioChip Technologies, Billerica, MA, USA).
Scanned images of microarray slides were analyzed numerically using the Agilent Feature Extraction Software.
Hybridization and washing of microarray slides (GPL7252, 43494 probes [Edgar et al. [2002]) were performed following manufacturer's protocols.
Pre-hybridization of microarray slides was previously described [24].
In the preparation of microarray slides the amount of DNA immobilized on the slide varies.
For the first set of microarray slides some slides were discarded due to uneven hybridisation.
For the microarray analysis, there were 3 technical replicates for each of the 3 biological samples, resulting in the use of nine microarray slides.
We examined NTSR1-ir in 2 independent cohorts of GIST using tissue microarray slides of formalin-fixed, paraffin-embedded (FFPE) material.
Two replicates of each experiment were performed using different microarray slides, in which sample and control RNA, labeled either with Alexa Fluor 555 or Alexa Fluor 647 fluorochromes, were crossed in both combinations (dye-swapping procedure).
Two replicates of each experiment were analysed using different microarray slides in which the sample and reference RNAs labelled with either Cy3 or Cy5 fluorochromes were crossed for both of the combinations.
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