Human Genome-Wide SpliceArrray - MAQC samples A, B, C, D

The human Genome-Wide SpliceArray (GWSA), a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale. The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC) Project. Four samples types (A, B, C, D) were hybridized in triplicate to the human Genome-wide SpliceArray platform resulting in a total of 12 data files. The sample types are those that were previously described and used in the Microarray Quality Control (MAQC) Project and include the following: Sample A = Universal Human Reference RNA; Sample B = Human Total Brain RNA; Sample C =a mixture of sample A and B RNAs - 75% sample A+25% sample B; Sample D =a mixture of sample A and B RNAs - 25% sample A+75% sample B. cDNA was amplified from the RNA samples, and subsequently fragmented and biotin-labeled. Prepared target from each of the 12 samples (4 sample types, 3 replicates each) was separately hybridized to 12 human Genome-wide SpliceArray (GWSA) products.