cell line: HCT116 cell type: Human colon cancer cells transferred chromosome: 8 ploidy: diploid
Extracted molecule
genomic DNA
Extraction protocol
Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.
Label
Biotin (C, G), DNP (A,T)
Label protocol
200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).
Hybridization protocol
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol
After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a iScan (Illumina).
Description
Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips
Data processing
Data processing was done using GenomeStudio (Illumina)
