The RNA amplification, chip hybridization and data extraction was done as a service by The Centre for Applied Genomics, Toronto, Canada.
Before and after library amplification, ChIP DNA between 200 and 500 bp was gel purified on 2% agarose and quantified using an Agilent 2100 Bioanalyzer.
In our study, we used the GenomePlex® Whole Genome Amplification ChIP-chip analyses and found that HBc can bind to more than three-thousand promoters in the human genome.
For instance, promoter microarray-based approaches include the methylated CpG island amplification microarray chip (MCAM-chip) that utilizes enzymatic digestion [ 5, 6] and the methylated DNA immunoprecipitation microarray chip (MeDIP-chip) that employs antibody pulldown [ 12] to enrich methylated DNA.
This chapter reviews the use of microelectronic-based techniques in molecular diagnostic assays with a focus on microfabrication, cell sorting, molecule preconcentration, sample preparation techniques, DNA/RNA amplification on chips, electronic-assisted hybridization assays, and examples of commercially available platforms.
To measure the effect of aRNA from different time-points of amplification, DNA chips containg 5760 features were hybridized to Cy3-labeled aRNA from 4 h and 16 h amplifications.
DNA amplification, fragmentation, chip hybridization, single base extension, staining and scanning were conducted by the Life Science and Technology Center, China National Seed Group Co., LTD (Wuhan, China).
Genomic DNA amplification, fragmentation, chip hybridization, washing, single-base extension through DNA ligation, and signal amplification was carried out according to Affymetrix Axiom® 2.0 Assay Manual Target Prep Protocol.
DNA amplification, fragmentation, chip hybridization, single base extension, staining and scanning were conducted by Life Science and Technology Center, China National Seed Group Co., LTD (Wuhan, China), according to Infinium HD Assay Ultra Protocol (http://www.illumina.com/).
In addition, from the data, we can interpret that amplification of ChIP DNA by LM-PCR prior to hybridization to the tiling array did not introduce a significant bias into the ChIP on chip results.
