Various factors (e.g., sample preparation, reagent quality) may influence hybridization of target mRNA to microarray probes, thus causing unreliable measurements of expression intensities.
We then used multidimensional scaling (MDS) to summarize the data from individual microarray probes and thus graphically represent the variability in the DNA methylation profiles between all the samples (Fig. 1B).
Any allele-specific events outside the microarray probe region will thus skew the comparison.
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 microarray probe design and validation procedure [ 32] was such that only probes that exhibited a reduction in signal intensity (and thus represent a non-binding/absent event) following inclusion of a three nucleotide mismatch were selected.
Jetset: Selecting the optimal microarray probe set to represent a gene.
The position of the transcript and corresponding microarray probe (if available) is indicated.
All the probe sequences contained their corresponding microarray probe sequences.
For example, the majority of microarray gene-expression platforms, including the platform used here, rely on 3'-biased amplification protocols and thus position microarray probes near the 3'-end of the gene.
The recent release of the tomato genome sequence allowed us to map the microarray probes on the genome sequence, thus providing the opportunity of a more accurate functional annotation of the array.
