Sample Analysis and Processing
Through Epigenetic mechanisms, a genome can dynamically respond to the environment, leading to heritable changes in gene expression that cannot be attributed to underlying DNA sequence. Examples of epigenetic mechanisms include histone modification and DNA methylation. Recent advances in technology enable us to combine classic biochemical techniques, such as chromatin immunoprecipitation and bisulfite treatment, with cutting edge microarray and Next-Generation Sequencing platforms to achieve genome-wide detection of epigenetic events.
Bisulfite Treatment (QPCR)
Treatment of DNA with bisulfite converts cytosine residues to uracil, but leaves 5-methylcytosine residues unchanged. The methylation status of treated DNA is then determined by methylation-specific PCR (MSP) or direct sequencing.
Illumina Infinium methylation arrays are used to interrogate methylation sites at single nucleotide resolution. Medium-throughput solutions interrogate >25,000 CpG loci covering 14,000 genes, while high-throughput options cover more than 450,000 expertly selected methylation sites.
Affymetrix GeneChip Tiling arrays offer a comprehensive solution for novel isoform discovery as well as mapping the sites of protein-DNA interactions in ChIP experiments.
Rapidly survey the binding sites of transcription factors and other chromatin-associated binding proteins that influence gene regulation. Chromatin immunoprecipitated DNA is readily converted into sequencing libraries and sequenced on the Illumina MiSeq Personal Sequencers and HiSeqTM 2000 platforms.
Rapidly and economically detect genome-wide methylation patterns by direct sequencing on the Illumina MiSeq Personal Sequencers and HiSeqTM 2000 platforms. A variety of methods exist, including sequencing of bisulfite-converted DNA, methylation-sensitive restriction digest-enriched fragments, or chromatin immunoprecipitates of methyltransferases bound to DNA.
Array-comparative genomic hybridization (Array CGH) enables high-resolution detection of genomic copy number variants. Differentially labeled reference and experimental samples are hybridized to microarrays, allowing detecting of structural variants as small as 200bp. A wide variety of Agilent microarrays are offered for those interested in array CGH.