Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Avian gut microbiome reflects spatial genetic structure in a small island population

ABSTRACT: Avian gut microbiome reflects spatial genetic structure in a small island population

PROVIDER: PRJEB59418 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR10829028_1.fastq.gz	Fastqsanger.gz
	ERR10829028_2.fastq.gz	Fastqsanger.gz
	ERR10829029_1.fastq.gz	Fastqsanger.gz
	ERR10829029_2.fastq.gz	Fastqsanger.gz
	ERR10829030_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Multi-layered population structure in Island Southeast Asians

Project description:The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognized major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers.

2016-02-04 | GSE77508 | GEO

Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

Project description:Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

| PRJNA473478 | ENA

Single-cell and spatial transcriptomics of the avian embryo tailbud

Project description:Single-cell and spatial transcriptomics of the avian embryo tailbud

| PRJEB74465 | ENA

Population Prehistory in Island Southeast Asia

Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.

2017-08-02 | GSE80534 | GEO

CpG island mediated linear and spatial gene partitioning (RNA-seq)

Project description:CpG island mediated linear and spatial gene partitioning (RNA-seq)

| PRJNA319992 | ENA

Expression reflects population structure.

Project description:Population structure in genotype data has been extensively studied, and is revealed by looking at the principal components of the genotype matrix. However, no similar analysis of population structure in gene expression data has been conducted, in part because a naïve principal components analysis of the gene expression matrix does not cluster by population. We identify a linear projection that reveals population structure in gene expression data. Our approach relies on the coupling of the principal components of genotype to the principal components of gene expression via canonical correlation analysis. Our method is able to determine the significance of the variance in the canonical correlation projection explained by each gene. We identify 3,571 significant genes, only 837 of which had been previously reported to have an associated eQTL in the GEUVADIS results. We show that our projections are not primarily driven by differences in allele frequency at known cis-eQTLs and that similar projections can be recovered using only several hundred randomly selected genes and SNPs. Finally, we present preliminary work on the consequences for eQTL analysis. We observe that using our projection co-ordinates as covariates results in the discovery of slightly fewer genes with eQTLs, but that these genes replicate in GTEx matched tissue at a slightly higher rate.

| S-EPMC6317812 | biostudies-literature

Avian arcopallium

Project description:Avian arcopallium

| PRJNA139189 | ENA

Avian E.coli

Project description:Avian E.coli

| PRJEB11955 | ENA

Multi-layered population structure in Island Southeast Asians

Project description:The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognized major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesianexpansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5kya we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

| EGAS00001001738 | EGA

CpG island mediated linear and spatial gene partitioning (other data sets)

Project description:CpG island mediated linear and spatial gene partitioning (other data sets)

| PRJNA319990 | ENA