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E-GEOD-61193 - JBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC

Status
Released on 26 November 2014, last updated on 28 November 2014
Organism
Homo sapiens
Samples (2)
Protocols (3)
Description
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
Experiment type
methylation profiling by high throughput sequencing 
Contacts
Xueguang Sun <xsun@zymoresearch.com>, Darany Tan, Libin Cui, Tzu H Chung, Xi-Yu Jia
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-61193.idf.txt
Sample and data relationshipE-GEOD-61193.sdrf.txt
Processed data (2)E-GEOD-61193.processed.1.zip, E-GEOD-61193.processed.2.zip
Links