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Of these, 27 tumors were also previously analyzed by expression profiling using oligonucleotide microarrays [ 6] [Figure 1].
Protein microarrays provide means of rapidly validating the genes identified by expression profiling using DNA microarrays, at the protein level.
Thus, de novo assembly using 454 technology or a combination of 454 and shorter read technologies [ 16], followed by expression profiling using short reads seems a reasonable approach.
In an earlier study, we have identified several porcine miRNAs applying a novel cloning strategy based on synthesis of concatamers [ 17] followed by expression profiling using a miRNA specific quantitative PCR approach [ 27].
This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species.
In complex organisms without sequenced genomes, de novo transcriptome assembly using a longer read sequencing technology followed by expression profiling using short reads is likely to provide comprehensive identification of adaptive variation at the expression level and sequence polymorphisms in coding regions.
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The differentially expressed miRNAs were determined by expression profiles using the OpenArray system and small RNA-Seq.
Using overexpression of miRNAs followed by global expression profiling using microarrays, they demonstrated a modest but significant downregulation of mRNA levels of genes that were enriched for the miRNA seed sequence.
Although intrinsic subtypes of breast cancer were originally defined by gene expression profiling using DNA microarrays, most archival formalin-fixed paraffin-embedded samples are not amenable to cDNA microarray and subsequent studies revealed that subtypes can be accurately determined using immunohistochemical as a surrogate for molecular classification (Nielsen et al, 2004; Carey et al, 2006).
To determine the biological impact of GC structure on GR transcription, primary TM 86 and TM 93 cells were treated with DEX, FA, TA, or a vehicle control and total RNA was isolated 24 hr later followed by gene expression profiling using Agilent Whole Human Genome Microarrays.
Moreover, we show, by means of expression profiling using oligonucleotide microarrays, that gene sets downregulated by our identified miRNAs (and that possess their cognate seed-binding regions) display highly significant overlap with genes downregulated by c-Myc in mES cells.
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