GSM4504890: Sample_NEUFAM41-11 Medip-Seq; Homo sapiens; MeDIP-Seq
Whole blood was collected in EDTA tubes and genomic DNA (gDNA) extraction was performed with phenol–chloroform standard method or with the Maxwell 16 blood DNA purification kit (Promega) according to manufacturer's protocol. Quantity and quality of gDNA were determined by Qubit BR dsDNA assay (ThermoFisher) and 1.5% agarose gel, respectively MeDIP: One μg of each gDNA sample was mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). Sequencing libraries were prepared with NextFlex Methylseq 1 kit (Bioo Scientific) according to the manufacturer's protocol MeDIP: The ligated libraries were pooled and immunoprecipitated in the same reaction using MagMeDIP kit (Diagenode), followed by purification with IPure v2 kit (Diagenode) and PCR amplification. Paired-end sequencing was performed on the Illumina HiSeq 2500 platform with read length of 100 bp. BiSulfite: A SeqCap Epi custom panel (Roche) was designed by NimbleDesign software (Roche).   Sequencing libraries were prepared with KAPA Hyper Prep kit (Kapa Biosystems) according to the manufacturer's protocol, starting from 1 μg of gDNA mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). After ligation, bisulfite conversion was performed by EZ DNA Methylation-Lighting kit (Zymo Research), followed by enrichment of the regions of interest with custom probes using SeqCap Epi enrichment kit (Roche).
GEO Accession
GSM4504890