Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Y-chromosome capture of ancient human samples

ABSTRACT: In-solution Y-chromosome capture-enrichment on ancient DNA libraries

PROVIDER: PRJEB23498 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2197970_1.fastq.gz	Fastqsanger.gz
	ERR2197970_2.fastq.gz	Fastqsanger.gz
	ERR2197971_1.fastq.gz	Fastqsanger.gz
	ERR2197971_2.fastq.gz	Fastqsanger.gz
	ERR2197972_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Homo sapiens

Project description:In-solution Y-chromosome capture-enrichment on ancient DNA libraries

| PRJNA419010 | ENA

In solution target enrichment for ancient DNA

Project description:Experimental conditions improving in solution target enrichment for ancient DNA

| PRJEB13983 | ENA

Ancient DNA hyRAD capture

Project description:Performance and automation of ancient DNA capture with RNA hyRAD probes.

| PRJEB43744 | ENA

Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

Project description:Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

2020-10-01 | GSE121623 | GEO

Chromosome conformation capture in Rif1 null pMEFs

Project description:Chromosome conformation capture in Rif1 null pMEFs

| PRJEB9110 | ENA

Systematic evaluation of chromosome conformation capture assays

Project description:Systematic evaluation of chromosome conformation capture assays

| PRJNA698572 | ENA

Extensive conservation of ancient microsynteny across metazoans

Project description:Gene order, or microsynteny, is generally thought not to be conserved across metazoan phyla. Only a handful of exceptions, typically of tandemly duplicated genes such as Hox genes, have been discovered. Here, we performed a systematic survey for microsynteny conservation in 17 genomes and identified nearly 600 pairs of unrelated genes that have remained together across over 600 million years of evolution. Using multiple genome-wide resources, including several genomic features, epigenetic marks, sequence conservation and microarray expression data, we provide extensive evidence that many of these ancient microsyntenic arrangements have been conserved in order to preserve either (i) the coordinated transcription of neighboring genes, or (ii) Genomic Regulatory Blocks (GRBs), in which transcriptional enhancers controlling key developmental genes are contained within nearby “bystander” genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos to further investigate putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results show that ancient genomic associations are far more common in modern metazoans than previously thought – likely involving over 12% of the ancestral bilaterian genome – and that cis-regulatory constraints have played a major role in conserving the architecture of metazoan genomes. ChIP-seq H3K27me3 of 24hpf zebrafish embryos

2012-06-21 | E-GEOD-35050 | biostudies-arrayexpress

Lapita ancient DNA

Project description:In-solution capture of 1.2 million SNP targets from ancient humans associated with the Lapita culture of Remote Oceania and Polynesia.

| PRJEB14728 | ENA

A Streamlined Tethered Chromosome Conformation Capture Protocol

Project description:Background: Identification of locus-locus contacts at the chromatin level provides a valuable foundation for understanding of nuclear architecture and function and a valuable tool for inferring long-range linkage relationships. As one approach to this, chromatin conformation capture-based techniques allow creation of genome spatial organization maps. While such approaches have been available for some time, methodological advances will be of considerable use in minimizing both time and input material required for successful application. Results: Here we report a modified tethered conformation capture protocol that utilizes a series of rapid and efficient molecular manipulations. We applied the method to Caenorhabditis elegans, obtaining chromatin interaction maps that provide a sequence-anchored delineation of salient aspects of Caenorhabditis elegans chromosome structure, demonstrating a high level of consistency in overall chromosome organization between biological samples collected under different conditions. In addition to the application of the method to defining nuclear architecture, we found the resulting chromatin interaction maps to be of sufficient resolution and sensitivity to enable detection of large-scale structural variants such as inversions or translocations. Conclusion: Our streamlined protocol provides an accelerated, robust, and broadly applicable means of generating chromatin spatial organization maps and detecting genome rearrangements without a need for cellular or chromatin fractionation.

2016-01-20 | GSE76930 | GEO

Systematic evaluation of chromosome conformation capture assays [1D]

Project description:Systematic evaluation of chromosome conformation capture assays [1D]

| PRJNA698732 | ENA