MethylCap kit

Protocol tips

Upstream tips	Protocol tips	Downstream tips
Always include fully methylated (in-vitro methylated DNA) and non-methylated controls (Leucocyte DNA, DNMT1/3 double KO DNA) during MSP

Upstream tips
Always include fully methylated (in-vitro methylated DNA) and non-methylated controls (Leucocyte DNA, DNMT1/3 double KO DNA) during MSP

Publication protocol

Bisulfite sequencing and Infinium BeadChip data
Reduced representation bisulfite sequencing [14] was performed by BaseClear (Leiden, the Netherlands), using the EpiQuest DNA Methylation Analysis Platform (http://www.baseclear.com/dna-sequencing/next-gen-sequencing/epiquest-5-mc-analysis/) yielding 2×50 paired end bisulfite sequence reads, with total coverages of 27.9, 39.2 and 51.0 million paired reads for respectively HCT15, PC3 and DU145 which were further processed using a custom pipeline (BaseClear). For each CpG, intensities for both strands of the genome were summed for comparison with MBD-seq data.

Independent Infinium HumanMethylation27 BeadChip data, as reported by Kim et al. [27], were downloaded from the Gene Expression Omnibus (GEO, accession number: GSE23388, data were already quantile normalized). R-package IlluminaHumanMethylation27k.db and GEO dataset GPL8490 were used to identify the exact location of each CpG assessed by the individual probes. The UCSC liftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) with standard settings was applied to convert CpG-loci from human reference genome build 36 to build 37, with a success rate of 99.95%.

Full paper   Login or join for free to view the full paper.

Reviews

Discussion

Papers

Check out relevant papers found by Labettor's AI that are relevant for performing DNA methylation profiling Whole genome profiling - HCT116, HTC15 human colon cancer cells using MethylCap kit from Diagenode.

Manufacturer protocol

Download the product protocol from Diagenode for MethylCap kit below.

Download manufacturer protocol

Videos

Check out videos that might be relevant for performing DNA methylation profiling Whole genome profiling - HCT116, HTC15 human colon cancer cells using MethylCap kit from Diagenode. Please note that these videos are representative and steps or experiment specific processes must be kept in mind to expect desired results.