Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lapita ancient DNA

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

PROVIDER: PRJEB14728 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1520024.fastq.gz	Fastqsanger.gz
	ERR1520025.fastq.gz	Fastqsanger.gz
	ERR1520026.fastq.gz	Fastqsanger.gz
	ERR1520027.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

South Pacific ancient DNA

Project description:Language continuity despite population replacement in Remote Oceania

| PRJEB24810 | ENA

Ancient dental calculus from Oceania

Project description:Ancient dental calculus from Oceania

| PRJEB61887 | ENA

Y-chromosome capture of ancient human samples

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

| PRJEB23498 | ENA

In solution target enrichment for ancient DNA

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

| PRJEB13983 | 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

An ancient residue metabolomics-based method to distinguish use of closely related plant species in ancient pipes

Project description:Residues from ancient artifacts can help identify which plant species were used for their psychoactive properties, providing important information regarding the deep-time co-evolutionary relationship between plants and humans. However, relying on the presence or absence of one or several biomarkers has limited the ability to confidently connect residues to particular plants. We describe a comprehensive metabolomics-based approach that can distinguish closely related species and provide greater confidence in species use determinations. An approximately 1430-year-old pipe from central Washington State not only contained nicotine, but also had strong evidence for the smoking of Nicotiana quadrivalvis and Rhus glabra, as opposed to several other species in this pre-contact pipe. Analysis of a post-contact pipe suggested use of different plants, including the introduced trade tobacco, Nicotiana rustica. Ancient residue metabolomics provides a new frontier in archaeo-chemistry, with greater precision to investigate the evolution of drug use and similar plant-human co-evolutionary dynamics.

2020-07-21 | MTBLS890 | MetaboLights

Ancient transcriptional regulators can easily evolve new pair-wise cooperativity

Project description:We investigate how a protein-protein interaction between two ancient transcriptional regulators (a homeodomain and MADS box protein) was gained approximately 200 million years ago in a clade of ascomycete yeasts that includes Saccharomyces cerevisiae. We combine deep mutational scanning of Matα2 with a functional selection for cooperative gene expression and tested millions of possible alternative evolutionary solutions to this interaction interface. Pooled Matα2 mutants were deeply sequenced before and after selection for functional Matα2-Mcm1 interaction. The changes in frequency of each variant allowed us to determine their relative fitness.

2023-06-01 | GSE233191 | GEO

Genomic History of the Solomon Islands

Project description:The aim of this study was to provide for a better understanding of the genetic relationships among and between populations of Near and Remote Oceania, with a focus on the initial settlement of the Solomon Islands and their role in the first dispersal of people from Near into Remote Oceania. Irina Pugach, Ana T Duggan, D Andrew Merriwether, FranÃƒÂ§oise R Friedlaender, Jonathan S Friedlaender, Mark Stoneking, "The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data", Molecular Biology and Evolution, Volume 35, Issue 4, April 2018, Pages 871Ã¢Â€Â“886

| EGAS00001006116 | EGA

Vanuatu2

Project description:Population Turnover in Remote Oceania Shortly After Initial Settlement

| PRJEB24938 | ENA

Ancient human parvovirus B19

Project description:Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

| PRJEB26712 | ENA