Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: CRISPR-based targeted haplotype-resolved assembly of a megabase region

PROVIDER: PRJNA789659 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17250928_1.fastq.gz	Fastqsanger.gz
	SRR17250928_2.fastq.gz	Fastqsanger.gz
	SRR17250929.fastq.gz	Fastqsanger.gz
	SRR17250929_1.fastq.gz	Fastqsanger.gz
	SRR17250929_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 22

Similar Datasets

CRISPR-based targeted haplotype-resolved assembly of a megabase region [EPIC]

Project description:Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

2022-11-15 | GSE192501 | GEO

CRISPR-based targeted haplotype-resolved assembly of a megabase region [WGBS]

2022-11-15 | GSE192499 | GEO

CRISPR-based targeted haplotype-resolved assembly of a megabase region

Project description:CRISPR-based targeted haplotype-resolved assembly of a megabase region

| PRJNA791665 | ENA

CRISPR-based targeted haplotype-resolved assembly of a megabase region [EPIC]

Project description:CRISPR-based targeted haplotype-resolved assembly of a megabase region [EPIC]

| PRJNA791666 | ENA

CRISPR-based targeted haplotype-resolved assembly of a megabase region [WGBS]

Project description:CRISPR-based targeted haplotype-resolved assembly of a megabase region [WGBS]

| PRJNA791667 | ENA

Complete Haplotype Phasing of the MHC and KIR Loci with Targeted HaploSeq

Project description:Rapid advances in biochemical technologies have enabled several strategies for typing candidate HLA alleles, but linking them into a single MHC haplotype structure remains challenging. Here we have developed a multi-loci haplotype phasing technique and demonstrate its utility towards phasing of MHC and KIR loci in human samples. We accurately (~99%) reconstruct the complete haplotypes for over 90% of sequence variants spanning the 4-megabase region of these two loci. By haplotyping a majority of coding and non-coding alleles at the MHC and KIR loci in a single assay, this method has the potential to assist transplantation matching and facilitate investigation of the genetic basis of human immunity and disease. Complete haplotype phasing of 2 loci (MHC and KIR) in 1 human cell line.

2016-02-01 | E-GEOD-65726 | biostudies-arrayexpress

Complete Haplotype Phasing of the MHC and KIR Loci with Targeted HaploSeq

2016-02-01 | GSE65726 | GEO

Homo sapiens strain:GM12878

Project description:Assembly-based structural variation and haplotypes from targeted sub-Megabase DNA molecules

| PRJNA430705 | ENA

A major genome region underlying artemisinin resistance in malaria

Project description:Evolving resistance to artemisinin-based compounds in SE Asia threatens to derail attempts to control and eliminate malaria. Resistance has been confirmed in western Cambodia, has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CR) from the blood following treatment. We used a two-phase approach to identify the genes underlying this ongoing selective event. Comparison of geographical differentiation and haplotype structure at 6,969 polymorphic SNPs in 91 parasites from western Cambodia, western Thailand and Laos identified 33 strongly selected genome regions. We screened SNPs and microsatellites within these genome regions in 718 parasites from western Thailand, and identified a 35kb region of chr 13 showing strong association (P=10-6 to 10-11) with slow CR. This region contains several compelling candidate loci, such as HSP70, for assessment by transfection. These results illustrate the efficacy of targeted association for identifying the genetic basis of adaptive traits.

2012-05-01 | GSE33002 | GEO

Project description:Haplotype-resolved Camellia gigantocarpa genome assembly

| PRJNA1047889 | ENA