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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.
In addition, single nucleotide polymorphisms (SNPs) were identified and mapped to trees, and SNP microarray probes were designed to enable highly multiplexed genotyping of an unsequenced sample by hybridization.
A total of 74,179 microarray probes were calibrated using the Gene Meter approach and the transcriptional profiles of 1063 genes that significantly increased in abundance were assembled into a time series spanning from life to 48 or 96 h postmortem.
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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The selection of microarray probes was performed in two steps using custom software developed in our lab.
This lack of enrichment indicates that hybridization artifacts due to SNPs within microarray probes are unlikely to affect our results.
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.
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.
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