Genomics

Dataset Information

240

JBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC


ABSTRACT: We developed a novel approach, J-binding protein 1 sequencing (JBP1-seq), that combines the benefits of an improved recombinant JBP1 protein, Nextera-based library construction, and nextgeneration sequencing (NGS) for genome-wide profiling of 5-hydroxymethylcytosine (5hmC). Compared with the original JBP1, this new recombinant JBP1 was biotinylatedin vivo and conjugated to magnetic beads via biotin-streptavidin interactions. These modifications allowed a more efficient and consistent pull-down of β-glucosyl-5-hydroxymethylcytosine (β-glu-5hmC), and sequence-ready libraries can be generated within 4.5 hours from DNA inputs as low as 50 ng. 5hmC enrichment of human brain DNA using the new JBP1 resulted in over 25,000 peaks called, which is significantly higher than the 4,003 peaks enriched using the old JBP1. Comparison of the technical duplicates and validations with other platforms indicated the results are reproducible and reliable. Thus, JBP1-seq provides a fast, efficient, cost-effective method for accurate 5hmC genome-wide profiling. An improvement of JBP1-Seq

ORGANISM(S): Homo sapiens  

SUBMITTER: Tzu H Chung   Xi-Yu Jia  Libin Cui  Darany Tan  Xueguang Sun 

PROVIDER: E-GEOD-61193 | ArrayExpress | 2014-11-26

SECONDARY ACCESSION(S): GSE61193SRP046311PRJNA260494

REPOSITORIES: GEO, ArrayExpress, ENA

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JBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC.

Cui Libin L   Chung Tzu Hung TH   Tan Darany D   Sun Xueguang X   Jia Xi-Yu XY  

Genomics 20140916 5


We developed a novel approach, J-binding protein 1 sequencing (JBP1-seq), that combines the benefits of an improved recombinant JBP1 protein, Nextera-based library construction, and next-generation sequencing (NGS) for genome-wide profiling of 5-hydroxymethylcytosine (5hmC). Compared with the original JBP1, this new recombinant JBP1 was biotinylated in vivo and conjugated to magnetic beads via biotin-streptavidin interactions. These modifications allowed a more efficient and consistent pull-down  ...[more]

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