Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates.
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.
Molecular techniques such as virus-specific polymerase chain reaction (PCR) or microarray hybridization capture provide even more powerful molecular enrichment for viral nucleic acid, but they require very specific prior knowledge about the sequence being sought that can hamper the discovery of highly novel pathogens (Tang and Chiu 2010; Mahony et al. 2011).
The hybridization signal and sequence data from the microarray hybridization experiment are provided in Additional file 8. Defect profiles for MMs and base bulges (Fig. 6) exhibit a very similar quantitative influence from defect position in DNA/DNA as well as in DNA/RNA complexes.
We thank Ina Poser and Martina Augsburg for BAC-tagging, Ina Nuesslein for FACS sorting of BAC transgenic ESC, Sabine Schmidt and Kathrin Saar for performing microarray hybridization, Rolf Jessberger for providing SMC1/SMC3 antibodies and critically reading the manuscript as well as Ronald Naumann for providing R1/E ESCs.
Incorporation of chromosome arm-specific microarray hybridization information is providing an important cross-reference for the positioning of genes in this framework.
DZ and ZL designed the study and wrote the manuscript, YW performed the fabrication of microarray and microarray hybridization, YB and QG provided the positive and negative clones of APC, MGMT, MLH1, TERT genes, YQ performed bisulfite modification and PCR, JL provided genomic DNA of colorectal cancer tissue samples, and CJ performed data analysis.
We performed BeadChip microarray hybridization according to the protocol provided by Illumina, using 20 Sentrix HumanRef-8 v2 BeadChip microarrays (Illumina, CA), 10 samples treated and 10 paired controls, loading 750 ng of cRNA onto each BeadChip.
Future microarray based approaches may make it possible to dispense with the genotyping of individuals entirely, provided that a very large number of SNPs can be multiplexed in a single microarray hybridization such that it immediately provides a reliable map position.
Thus it seems that our microarray hybridization approach is capable of providing information about A. niger gene expression modulation with a considerably high level of confidence.
