The identification of differentially expressed genes or patterns of gene expression using a microarray hybridization assay provides a logical approach to developing potential biomarkers of toxicity.
By hybridizing DNase I-digested fragments to tiled microarrays, the DNase-chip assay provides an undirected, unbiased, highly sensitive and specific strategy to simultaneously identify thousands of DHSs within any region of interest or even the entire genome, with a resolution of 200 500 bases [ 7].
As judged by the signal-to-noise ratios, the microarray-based assay provided signals at least in the range of the in-well assay.
This assay provides extensive allergen sensitization information while using only limited resources, supporting the hypothesis that allergen microarray technology is a more efficient and economically feasible diagnostic that currently used approaches.
More detailed explanation of microarray assays is provided in Additional file 1. Ingenuity Pathway Analysis 8.5 (IPA) (Ingenuity Systems, Redwood City, CA, USA) was used to select, annotate and visualize genes by function and pathway (gene ontology).
For more rigorous validation and testing they were tested again by the IP microarray assay in duplicate, providing 2 additional replicates of each.
P.S performed the TRKO library screening and partial functional study; K.K and D.L performed the most of functional studies, morphological studies, Q-PCR and microarray data analysis; N.S and D.L performed microarray assay; R.C and D. L provided the theoretical framework and guidance for this study and wrote the manuscript.
Tissue slide-based assays can be more cost effective in screening the expression of selected miRNAs (n < 10) in a large number of tissue samples (n > 500) using tissue microarrays, whereas RT-PCR assays provide high throughput in terms of the number of independent miRNAs (n > 100) that can be detected in a single tube reaction.
The procedure for the microarray assay was performed according to protocols provided by the manufacturer.
The data provide valuable information for DNA microarray assay developers.
