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

Spirodela polyrhiza

Project description:Spirodela polyrhiza clone 9509 sequenced with Oxford Nanopore

| PRJEB27612 | ENA

Discovery of novel and conserved microRNAs in Spirodela polyrhiza by deep sequencing

Project description:MicroRNAs (miRNAs) are a class of small, endogenous non-coding RNAs, which play key roles in a variety of developmental and physiological processes by regulating gene expressions at post-transcriptional or translational levels. The objective of our work was to explore conserved and novel miRNAs in Spirodela at the whole-genome level, and further characterize their potential roles in gene regulation. 1 sample

2014-02-21 | E-GEOD-55208 | biostudies-arrayexpress

Role of OxyR in Prevotella intermedia

Project description:Wild type Prevotella intermedia OMA14 strain (V3203) was used to compare to the OxyR-deficient strain (V3147).

2021-03-31 | GSE168003 | GEO