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This lack of enrichment indicates that hybridization artifacts due to SNPs within microarray probes are unlikely to affect our results.
This fraction also contains transcripts for which microarray probes are not performing as intended, which further reduces the number of potentially silent genes almost to none.
cDNA microarray probes are two different kinds containing exon 23 or intron 4. The probes containing exon 23 detect all known isoform expressions except GABAB1j.
Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs).
The microarray probes are from Xia et al. [ 11].
Many of the tobacco microarray probes are identified only by EST codes in the manufacturer's specifications.
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Microarray probes were matched to gene identifiers using the CDF array annotation (version 18) provided by the University of Michigan microarray© lab56.
First, microarray probes were optimized by screening 244,000 probes for hybridization with RNA from infected and uninfected macrophages.
The target gene regions of microarray probes were retrieved from the annotation file for human U133 Plus 2.0 (http://www.affymetrix.com).
Microarray probes were designed primarily from P. taeda hybridised with cRNA constructed from the close relative P. radiata.
The "present" and "absent" information of microarray probes were obtained by applying the mas5calls function in biocondutor (http://www.bioconductor.org).
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