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Understanding population genetics and patterns of genome wide heterozygosity in a sample of the Croatian isolated populations ESGIDalmatians

ABSTRACT: Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the population genetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who were selected to reflect islanders with at least four known ancestors in grandparental line who are original islanders.

PROVIDER: EGAS00001000336 | EGA |

REPOSITORIES: EGA

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EGAS00001000336-sc-20150601 - samples

Project description:Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the population genetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who were selected to reflect islanders with at least four known ancestors in grandparental line who are original islanders.

| EGAD00001001387 | EGA

Genomic evidence for the Pleistocene and Recent population history of Native Americans

Project description:How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Native Americans diversified into two basal genetic branches around 13 KYA, one in North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians and Australo-Melanesians, the latter possibly through the ancestors of Aleutian Islanders. Putative relict populations in South America, including the historical Pericúes and Fuego-Patagonians, are not directly related to modern Australo-Melanesians.

2015-07-20 | GSE70987 | GEO

Influence of RD2 on gene expression in serotype M1 and M49 GAS isolates

Project description:We used RNA-Seq to assess how the presence/absence of the RD2 pathogenicity island influences global gene expression in the parental serotype M1 GAS isolate MGAS2221 and the parental serotype M49 isolate NZ131

2021-03-12 | GSE167343 | GEO

POWV isolate from Long Island infects brain endothelial cells and pericytes. [hBVPs]

Project description:POWV isolate from Long Island (POWV-LI-9) is released basolaterally from humban brain microvascular endothelial cells (hBMECs) and infects primary human brain vascular pericutes (hBVPs).

2021-06-08 | GSE176252 | GEO

POWV isolate from Long Island infects brain endothelial cells and pericytes. [hBMECs]

2021-06-08 | GSE176251 | GEO

Intra-sample heterogeneity of sperm DNA methylation

Project description:Genome wide DNA methylation profiling of 2 distinct subpopulations of sperm within a single ejaculate. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples were provided by 20 normozoospermic individuals. A density gradient centrifugation was performed on each samples to yeild two distict populations for each ejaculate (one from the 90% isolate layer high quality sperm and one from the 35% isolate layer low quality sperm of the column).

2015-01-31 | GSE64096 | GEO

Wise Ancestors

Project description:Wise Ancestors

| PRJEB96280 | ENA

Genome-wide circular RNA expression patterns reflect resistance to immunomodulatory drugs in multiple myeloma cells

Project description:Immunomodulatory drugs (IMiDs), such as lenalidomide and pomalidomide, may induce significant remissions in multiple myeloma (MM) patients, but relapses are frequently observed and the underlying molecular mechanisms for this are not completely understood. Circular RNAs (circRNAs) constitute an emerging class of non-coding RNAs with important roles in cancer. Here, we profiled genome-wide expression patterns of circRNAs in IMiD sensitive MM cells and their resistant counterparts as well as in IMiD resistant cells treated with specific epigenetic drugs alone or in combination. We found that genome-wide circRNA expression patterns reflect IMiD-sensitivity and ciRS-7 (also known as CDR1as) was the most downregulated circRNA upon acquired resistance. The depletion of ciRS-7 correlated with increased methylation levels of the promoter CpG island of its host gene, LINC00632. Expression of LINC00632 and ciRS-7 was partly restored by treatment with a combination of an EZH2 inhibitor (EPZ-6438) and a DNA methyl transferase inhibitor (5-azacytidine), which also restores the IMiD sensitivity of the cells. However, knockdown of ciRS-7 did not affect IMiD sensitivity and we found that ciRS-7 also becomes epigenetically silenced after prolonged cell culture without drug-exposure. In conclusion, we found that genome-wide circRNA expression patterns reflect IMiD sensitivity in an in vitro model of acquired resistance.

2021-02-19 | GSE161960 | GEO

RD2-mediated regulation of gene expression following GAS exposure to human plasma

Project description:We used RNA-Seq to assess how the presence/absence of the RD2 pathogenicity island influences global gene expression in a serotype M28 GAS isolate following exposure to human plasma for 15 mins and for 60 mins

2024-08-12 | GSE138408 | GEO

Gene expression patterns in multispecies biofilm

Project description:Distinct patterns in global gene expression reflect synergy in a multispecies biofilm

| PRJEB12332 | ENA