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Series GSE48592 Query DataSets for GSE48592
Status Public on Nov 03, 2013
Title Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary 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.
Overall design Hi-C experiments in two replicates of Human GM12878 Lymphoblastoid cells and two replicates of F123 mouse ES cells (4 total samples)
Contributor(s) Dixon JR, Selvaraj S, Ren B
Citation(s) 24185094
Submission date Jul 08, 2013
Last update date Feb 22, 2021
Contact name Jesse R Dixon
Organization name Salk Institute for Biological Studies
Street address 10010 N. Torrey Pines Rd.
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1181865 Hi-C, F123 mouse ES cells, replicate one
GSM1181866 Hi-C, F123 mouse ES cells, replicate two
GSM1181867 Hi-C, GM12878 Lymphoblastoid cells, replicate one
BioProject PRJNA210760
SRA SRP026610

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE48592_F123.haps.txt.gz 62.4 Mb (ftp)(http) TXT
GSE48592_GM12878_depristoeal.vcf.txt.gz 26.4 Mb (ftp)(http) TXT
GSE48592_GM12878_lcp.vcf.txt.gz 28.2 Mb (ftp)(http) TXT
GSE48592_GM12878_seed.haps.txt.gz 2.2 Mb (ftp)(http) TXT
GSE48592_castx129_variants.vcf.txt.gz 206.1 Mb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA

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