Dataset features

Specifications


Application: BS-seq analysis
Number of samples: 2
Release date: Sep 13 2016
Last update date: Nov 27 2018
Access: Public
Dataset link Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) analysis using SureSelectXT Methyl-Seq Target Enrichment System

Experimental Protocol


Colon cancer cell line, HCT116, was treated GpC methyltransferase (M.CviPI) to methylate all GpC sites in the open chromain. The genomic DNA was then analyzed by targeted bisulfite sequencing. Oligo capture probes are designed to target 84Mb sequences covering 3.7 million CpGs including CpG islands, Cancer, tissue specific DMRs, Gencode promoters, DMRs or regulatory feature in CpG islands, shores, and shelves ±4kb, DNase I hypersensitive sites, Refseq genes, Ensembl regulatory features. The CAME package was used for analyzing the targeted NOMe-seq data. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data.

Repositories


GEO

GSE86823

ENA

SRP089703

BioProject

PRJNA342636

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Contact


Huidong Shi