SCGC Gene Methylation

The SCGC operates an Illumina BeadLab 1000, a LIMS supported laboratory system capable of processing custom snp, whole genome snp genotyping, methylation profiling as well as custom and whole genome gene expression profiling.
In support of our methylation services the SCGC has recently invested in an iScan scanner, aotuloader, additional Tecan robotics and a SciGene little dipper array processing robotic workstation. These capital improvements have resulted in a greatly increased methylation  chip processing capacity as well as increased reproducibility and consistency. The facility is capable of running all current Illumina products designed for the BeadArray or iScan readers and can process up to 576 whole genome methylation samples per day.

Illumina whole genome methylation profiling protocols begin with 500ng to 1ug of genomic DNA isolated from whole blood or tissue. All samples are quanted using a Picoogreen fluorescent assay and normalized to 50 ng/ul prior to Bisulfite conversion . Bisulfite conversion is accomplished using the Zymo EZ kit protocol and reagents. Converted DNA then proceeds into Illumina Infinium whole genome genotyping protocol and ultimately is hybridized to Methylation -27 chips, which are read on the iScan reader. The protocol takes 4 days to complete.  Beta( methylation ) values are reported in flat file format suitable for analysis in many 3rd party applications. Copies of the GenomeStudio( Illumina) project and raw data are also made available.

The SCGC currently supports all Illumina methylation products including Human Methylation -27 chips GoldenGate custom methylation assays.

Contact and Booking Details

Contact Nelson Freimer for details at or 310-794-9571. Cost estimates and information regarding the genotyping process and SNP pool design may be obtained by contacting Joe DeYoung, the facility manager at: or by phone at 310-825-2390