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In contrast, on w m4e and w m51b almost all microarray probes in this region report elevated levels of HP1.
In this visualisation we also plot the probe-specific expression levels for those genes with multiple microarray probes in the model derivation dataset.
Affymetrix probes and microarray probes in general tend to be designed against 3' ends of transcripts [ 24], mostly on the basis of EST evidence from NCBI's UniGene.
Figure 2 displays the distribution of microarray probes in relation to the distance from the 3' UTR for all transcripts present on both the KRM1 and KRM2 arrays.
We demonstrate the utility of the technology by applying it to generate more than 21 000 short (150 – 500 bp) and highly specific Arabidopsis gene sequence tags for use as microarray probes in transcriptional profiling.
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GABAB1j and GABAB1k were also only possible isoform models that contain the microarray probe in intron 4. Thus, #2, #3, #4, #11, and #18 can be partial GABAB1j or GABAB1k, and mRNAs containing the probe regions exist in human, mouse, and rat.
The Q-RT-PCR assays were designed to specifically amplify a region of the transcript different from that covered by the microarray probe in order to obtain an independent measurement.
The microarray probes used in the studies in Oncomine do not distinguish between neonatal and adult SCN5A splice variants.
The microarray probes used in the present study were based on the EGDe strain (Accession No. A-BUGS-19; http://bugs.sgul.ac.uk/A-BUGS-19).
PP helped designing SLICSel and the microarray probes, helped in data analysis and drafted the manuscript.
Microarray probes absent in more than 80% of samples based on an Illumina BeadStudio detection P_value >0.01 were removed from further analysis.
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