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Not only have we demonstrated the overall similarity of results obtained by deep sequencing and microarray hybridization of the same samples, but we have also shown that both sets of results are in strong agreement with existing knowledge of this cancer.
Microarray hybridization of DNA from different accessions can reveal differences between them--single-feature polymorphisms (SFPs).
Potential target genes regulated by a given miRNA were identified by in silico prediction and microarray hybridization of Ago2 coimmunoprecipitates.
Microarray hybridization of samples and references to the ChillPeach microarray slides was performed manually using Telechem Hybridization Chambers (Corning), following the manufacturer's instructions.
Total RNA isolation, target preparation and microarray hybridization of the Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were performed as described by Jennen et al. [ 40].
For microarray hybridization of DNA from individual adult Nasonia, including SILs, DNA was extracted using the QIAGEN Puregene Gentra protocol for single Drosophila (http://www.qiagen.com/literature).
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For this reason we performed microarray hybridization on a subset of the 1,999 MPH-correlated genes.
To compare the empty vector and RNAi vectors, a contrast test was applied taking the normalized log2 ratios of the three microarray hybridizations of each type as replicates against the same common control reference using BANAL, a web-based interface also running on Limma.
Microarray hybridizations of 51 breast cell lines were performed using the Agilent Human 1A V1 array.
Subsequently, material from the same batch of plants was used for dual-color microarray hybridizations of stressed and FN samples.
Comparison of our data to the report of gene absence from the microarray hybridizations of Stabler et al [ 17] highlights the problematic nature of reporting negative hybridization results.
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