DNA methylation in whole blood was profiled using methylated DNA immunoprecipitation sequencing (MeDIP-seq) in the TwinsUK cohort, as previously described.37 (link),38 (link) TwinsUK participants included the current MCC-seq study datasets were excluded from the TwinsUK MeDIP-seq dataset, resulting to a final independent TwinsUK MeDIP-seq dataset consisting of 116 T2D cases and 3318 controls. As previously described,38 (link) sonication was used to fragment DNA, following which libraries were prepared using Illumina's DNA Sample Prep kit for single-end sequencing. Immunoprecipitation was then carried out using anti-5mC antibody (Diagenode) and qPCR used for validation. Captured DNA underwent purification and amplification, following which 200-500bp fragments were selected. Sequencing was then carried out using the Illumina Platform and aligned using BWA.39 (link) Methylation levels were quantified using MEDIPS v1.0.40 (link) After processing, MeDIPseq data was quantified in bins of 500bps with a 250bp overlap.
Other organizations :
King's College London, The Open University, Inserm, Université Paris Cité, Sorbonne Paris Cité, Assistance Publique – Hôpitaux de Paris, Icahn School of Medicine at Mount Sinai, Karolinska Institutet, Children's Mercy Hospital, Chang Gung University, Chang Gung Memorial Hospital, Sir Charles Gairdner Hospital, University of Western Australia, Universidad de Murcia, UNSW Sydney, University of Helsinki, Helsinki University Hospital, Institute for Molecular Medicine Finland, Minerva Foundation, University of Southern Denmark, Vrije Universiteit Amsterdam
Participant selection: TwinsUK participants included in the current MCC-seq study datasets were excluded from the TwinsUK MeDIP-seq dataset, resulting in a final independent TwinsUK MeDIP-seq dataset.
DNA fragmentation: Sonication was used to fragment DNA.
Methylation detection: Immunoprecipitation was carried out using anti-5mC antibody and qPCR was used for validation.
Sequencing: Sequencing was carried out using the Illumina Platform and aligned using BWA.
Data quantification: Methylation levels were quantified using MEDIPS v1.0.
positive controls
None explicitly mentioned
negative controls
None explicitly mentioned
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