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Homo sapiens

ABSTRACT: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq]

PROVIDER: PRJNA369396 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5219980_1.fastq.gz	Fastqsanger.gz
	SRR5219980_2.fastq.gz	Fastqsanger.gz
	SRR5219981_1.fastq.gz	Fastqsanger.gz
	SRR5219981_2.fastq.gz	Fastqsanger.gz
	SRR5219982_1.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq]

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Project description:Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [HumanMethylation450]

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Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution

Project description:High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples represents a continuous challenge. Here, we present CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the hESC genome and base-resolution hydroxymethylome in human cell-free DNA.

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High grade glioma methylation analysis using bisulfite and oxidative bisulfite-treatment

Project description:Bisulfite and oxidative bisulfite treated sample methylation analysis of IDH1 mutant and wild-type high grade human gliomas, to profile 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Genomic DNA isolated directly from fresh-frozen human high grade glioma specimens.

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Intronic Non-CG DNA Hydroxymethylation and Alternative mRNA Splicing in Honey Bees

Project description:Honey bee non-CG DNA hydroxymethylation is enriched in the introns, which supplements previous findings that honey bee CG DNA methylation is enriched in exons. Bisulfite sequencing combined with Pvu-Seq to distinguish 5-methylcytosine from 5-hydroxymethylcytosine and RNA-Seq

2013-09-19 | E-GEOD-50990 | biostudies-arrayexpress

Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing

Project description:5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on the oxidative DNA demethylation pathway and is implicated in regulation of embryogenesis, neurological processes and cancerogenesis. Profiling of this relatively scarce genomic modification in clinical samples requires cost-effective high resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single nucleotide resolution, named hmTOP-seq, which is based on direct sequence readout primed at covalently labeled 5hmC sites from an in situ tethered DNA oligonucleotide. Examination of distinct tethering chemistries suggested a putative model for the targeted non-homologous polymerase priming which permits theoretical evaluation of suitable tethers at the design stage. The robustness and resolution of hmTOP-seq was validated on a small model genome and mouse embryonic stem cells, which allowed construction of single nucleotide 5hmCG maps that reflect subtle differences in strand-specific CG hydroxymethylation. Collectively, hmTOP-seq expands the toolbox of valuable techniques for cost-effective identification of epigenetic changes and new disease biomarkers.

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A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

Project description:We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence. Bisulfite-converted DNA for 2,664 human samples and 36 technical replicates were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2.

2015-01-22 | E-GEOD-55763 | biostudies-arrayexpress

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Project 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

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