Microarray Comperative genomic hybridization - Mouse iPSC

DNA microarrays enable researchers to monitor the expression of thousands of genes simultaneously. However, the sensitivity, accuracy, specificity, and reproducibility are major challenges for this technology. Cross-hybridization, combination with splice variants, is a prime source for the discrepancies in differential gene expression calls among various microarray platforms. Removing (either from production or downstream bioinformatic analysis) and/or redesigning the microarray probes prone to cross-hybridization is a reasonable strategy to increase the hybridization specificity and hence, the accuracy of the microarray measurements.

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Protocol tips
Each labeled miPSC DNA was hybridized together with the labeled donor DNA onto Agilent SurePrint G3 mouse 1 × 1 M microarray for 40 hours at 65°C. DNA processing, microarray handling and scanning were conducted following the Agilent oligonucleotide CGH protocol (version 6.0).
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