Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Vidua chalybeata (Village indigobird) genome, bVidCha1, sequence data.

PROVIDER: PRJNA1007608 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25708845.fastq.gz	Fastqsanger.gz
	SRR25708846.fastq.gz	Fastqsanger.gz
	SRR25708847_subreads.fastq.gz	Fastqsanger.gz
	SRR25708848_subreads.fastq.gz	Fastqsanger.gz
	SRR25708849_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 31

Similar Datasets

Project description:Vidua chalybeata (Village indigobird) genome, bVidCha1

| PRJNA912708 | ENA

Vidua chalybeata isolate:bVidCha1

Project description:Vidua chalybeata (Village indigobird) genome, bVidCha1, merged haplotype

| PRJNA889055 | ENA

Vidua chalybeata isolate:bVidCha1

Project description:Vidua chalybeata (Village indigobird) genome, bVidCha1, purge dup haplotype

| PRJNA889056 | ENA

Vidua chalybeata strain:NA

Project description:Vidua chalybeata

| PRJNA969777 | ENA

Village In a Dish: A Model System for Population-scale hiPSC Studies [Affymetrix]

Project description:The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and under different conditions. Human induced pluripotent stem cells (hiPSCs) are uniquely suited to study these context-dependent effects, but to do so requires cell lines from hundreds or thousands of individuals. Village cultures, where multiple hiPSC lines are cultured and differentiated in a single dish, provide an elegant solution for scaling hiPSC experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned back to a donor line using single-cell sequencing and addressing whether line-specific signalling alters the transcriptional profiles of companion lines in a village. We generated single-cell RNA sequence data from hiPSC lines cultured independently (uni-culture) and in villages at three independent sites. Using a mixed linear model framework, we estimate that the proportion of transcriptional variation across cells is predominantly due to donor effects, with minimal evidence of variation due to culturing in a village system. We demonstrate that the genetic, epigenetic or hiPSC line-specific effects explain a large percentage of gene expression variation for many genes, not the village status. This is reiterated by replication of previously identified genetic effects. Finally, we demonstrate consistency in the landscape of cell states between uni- and village-culture systems. We demonstrate that village methods can effectively detect hiPSC line-specific effects, including sensitive dynamics of cell states.

2023-02-14 | GSE224950 | GEO

Vidua chalybeata

Project description:The village indigobird is a brood parasite on another bird species.

| PRJNA10833 | ENA

Village In a Dish: A Model System for Population-scale hiPSC Studies [scRNA-Seq]

2023-02-14 | GSE225278 | GEO

Project description:Indigobird transcriptome

| PRJNA820299 | ENA

Expression profiling in lymphoblastoid cell lines of family with maternally inherited non-syndromic hearing loss.

Project description:We analyzed samples from fourteen deaf individuals (Affected 1 through 14), fifteen hearing maternally related family members (Unaffected 1-15), six marry-in controls (Controls 1-6) from extended pedigree from Arab-Israeli village, and nine individuals from another Arab-Israeli village (Controls 7-15). All affected and unaffected maternally-related individuals carry homoplasmic mutation in the 12S rRNA gene of the mitochondrial DNA, associated with both non-syndromic and aminoglycosides-induced deafness. Keywords: Comparison of genome-wide expression in cell lines of maternally-related individuals with mitochondrial mutation and controls carrying wild-type mitochondrial chromosome.

2009-06-01 | GSE9822 | GEO

Vidua larvaticola strain:NA

Project description:Vidua larvaticola

| PRJNA969783 | ENA