A total of 27 samples were submitted for DNA methylation array analysis, including samples from each of the three cell lines treated with vehicle controls (n = 3 per cell line), DIM (n = 3 per cell line), and SFN (n = 3 per cell line). Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA). For genomic DNA fragmentation, purified DNA was digested with MseI restriction enzyme (New England Biolabs, Ipswich, MA) overnight at 37°C to yield DNA fragments between 200 to 1,000 bp. Methylated DNA was enriched using methyl-DNA immunoprecipitation (MeDIP) according to manufacturer’s protocol (Roche NimbleGen, Madison, WI). MeDIP-enriched DNA as well as input DNA was amplified with GenomePlex Complete Whole Genome Amplification kit (Sigma). Amplified MeDIP and input DNA samples were submitted to Center for Genome Research & Biocomputing core facility (Oregon State University, Corvallis, OR) for sample labeling, sample hybridization, and array scanning. Sample hybridization and array scanning were done using NimbleGen Hybridization System 4 (Roche) and Axon GenePix Pro 4200 A (Molecular Device, Sunnyvale, CA), respectively.
Nimblegen hybridization system 4
Manufactured by Roche
The NimbleGen Hybridization System 4 is a laboratory equipment designed for use in microarray analysis. It facilitates the hybridization of labeled samples to microarray slides in a controlled and automated manner.
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Lab products found in correlation
2 protocols using nimblegen hybridization system 4
1
DNA Methylation Array Analysis of Cell Lines
2
NimbleGen Microarray Analysis Protocol
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NimbleGen microarray (Roche NimbleGen, Inc.) was detected by Shanghai Kang-Chen Biotechnology. A total of six microarrays were used, including three biological replicates for HeLa-NC and HeLa-630 cells. The NimbleGen Hybridization System 4 (Roche NimbleGen, Inc.) was used for hybridization. The hybridization reaction was performed using a hybridization kit (Roche NimbleGen, Inc.) in accordance with NimbleGen's instructions. Once the reaction was complete, the array was subjected to elution using a Wash Buffer kit (Roche NimbleGen, Inc.) and spun dry by centrifugation (200 × g, 25°C, 5 min).
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