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The unique signal pattern obtained by hybridizing each sample pair (individual clone and reference) to the genotyping array was recorded as "0" or "1".
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The gene expression profile for each sample was generated by labelling and hybridizing each sample to one of 16 separate microarrays.
There are several commercially available platforms that measure gene expression by hybridizing a labelled sample to a set of DNA probes, and their details can differ from the preceding description.
To save costs, we have reused the arrays up to three times by hybridizing different samples.
Transcriptome analysis was performed by hybridizing all samples comprising the experimental design on both the TOM1 and apple arrays containing 12,899 and 1,608 ESTs, respectively (Additional file 1).
All validation datasets (consisting of six GeneChips each) were produced by hybridizing triplicate RNA samples from a breast cancer cell line (MCF7) and an immortalised normal breast cell line (MCF10A) using a variety of different array types and sample preparation protocols.
Transcriptional activity in K562 and U937 was determined by hybridizing samples to the Affymetrix U133 plus 2.0 gene expression microarray and also to the Sanger ENCODE array.
Hepatic gene expression was assessed by hybridizing samples to Agilent 4 × 44 k Whole Genome Microarrays (G4122F) using a reference design (details below).
The amount of sequence diversity presented in Figure 4 supports the idea that individual integration sites (loci) and alleles of repetitive elements can be uniquely identified by high-throughput array based assays by hybridizing samples to short probes.
Over the last several years, great strides have been made in expanding the use of ChIP from a one gene-at-a-time approach to a global type of analysis by hybridizing samples to genomic microarrays (i.e., ChIP-on-chip assay) [ 26].
A hybridization time course was performed by hybridizing the same cRNA sample to separate arrays, each array hybridized for different times, and examining the hybridization intensities for endogenous transcripts.
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