Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

ABSTRACT: Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

PROVIDER: PRJNA210760 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

Project description:Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype remains a challenge. An understanding of complete haplotypes of an individual will help clarify the consequences of inheriting multiple alleles in combination, identify novel disease associations, and augment studies of gene regulation. Although numerous methods have been developed to reconstruct haplotypes from WGS data, chromosome-span haplotypes at high resolution have been difficult to obtain. Here we present a novel method to accurately reconstruct chromosome-span haplotypes from proximity-ligation and DNA shotgun sequencing. We demonstrate the utility of this approach in producing high-resolution chromosome-span haplotype phasing in mouse and human. While proximity-ligation based methods were originally designed to investigate spatial organization of the genome, our results lend support for their use as a general tool for haplotyping in the future. Hi-C experiments in two replicates of Human GM12878 Lymphoblastoid cells and two replicates of F123 mouse ES cells (4 total samples)

2013-11-03 | E-GEOD-48592 | biostudies-arrayexpress

Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

2013-11-03 | GSE48592 | GEO

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.

Project description: Not available

| S-EPMC4180835 | biostudies-literature

RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

Project description:We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum.

2023-04-07 | GSE209901 | GEO

RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

Project description:RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

| PRJNA285680 | ENA

Mapping of Long-Range Chromatin Interactions using Proximity Ligation Assisted ChIP-seq

Project description:We report Proximity Ligation Assisted ChIP-sequencing (PLAC-seq), a method for comprehensive detection of long-range interactions associated with proteins of interest. PLAC-seq requires up to 500-fold less starting material compared to ChIA-PET and using experimentally determined input as control precisely reveals protein associated interaction upto single-element resolution. Application of PLAC-seq to mouse embryonic stem cells revealed a comprehensive map of regulatory interactions.

2016-11-15 | GSE86150 | GEO

Employing proximity-dependent ligation techniques to estimate EcR/Usp molecular partners in Drosophila

Project description:Employing proximity-dependent ligation techniques to estimate EcR/Usp molecular partners in Drosophila

| PRJNA579279 | ENA

RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

Project description:Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing

2015-08-01 | GSE69472 | GEO

RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

Project description:Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing Proof-of-concept of RPL in S. cerevisiae and H. sapiens tissue culture

2015-08-01 | E-GEOD-69472 | biostudies-arrayexpress

Integrative analysis of haplotype-resolved epigenomes across human tissues

Project description:Allelic differences between the two sets of chromosomes can affect the propensity of inheritance in humans, but the extent of such differences in the human genome has yet to be fully explored. Here, we delineate allelic chromatin modifications and transcriptomes amongst a broad set of human tissues, enabled by a chromosome-span haplotype reconstruction strategy1. The resulting haplotype-resolved epigenomic maps reveal extensive allele bias in the transcription of human genes as well as chromatin state, allowing us to infer cis-regulatory relationships between genes and their control sequences. These maps also uncover a new class of cis regulatory elements and detail activities of repetitive elements in various human tissues. The rich datasets described here will enhance our understanding of the mechanisms controlling tissue-specific gene expression programs. One replicate of Hi-C experiment in four human tissues with four different individuals (Thymus STL001, Aorta STL002, Leftventricle STL003, and Liver STL011).

2015-02-18 | E-GEOD-58752 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data