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PP helped designing SLICSel and the microarray probes, helped in data analysis and drafted the manuscript.
LK designed SLICSel and microarray probes, helped with microarray data analysis and drafted the manuscript.
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Improvement of microarray probe design may help to circumvent the bias introduced by the amplification method, which is currently not optimal for samples with limited amounts of RNA.
Fig. 3 Transcripts identified in RAP annotations and 44 K microarray probes.
In both root and shoot samples, about 95% of transcripts were supported by the microarray probes.
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 design employed microarray probes optimized for uniformity, sensitivity, and specificity, with probe properties computed using the latest thermodynamic models.
Heterologous hybridisation requires microarray probes that are capable of tolerating a certain degree of mismatch with the target transcripts.
First, microarray probes were optimized by screening 244,000 probes for hybridization with RNA from infected and uninfected macrophages.
GB2 sets were specific for other microarray probes containing intron 4. The probes were human cDNA microarray clone 300899 and its mouse homologs.
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