Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA934891 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23455900_1.fastq.gz	Fastqsanger.gz
	SRR23455900_2.fastq.gz	Fastqsanger.gz
	SRR23455901_1.fastq.gz	Fastqsanger.gz
	SRR23455901_2.fastq.gz	Fastqsanger.gz
	SRR23455902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 111

Similar Datasets

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

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

2023-02-14 | GSE225278 | GEO

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

Project description:Village In a Dish: A Model System for Population-scale hiPSC Studies

| PRJNA934883 | ENA

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

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

| PRJNA934890 | ENA

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-02-14 | GSE225282 | GEO

A village in a dish model system for population-scale hiPSC studies.

| S-EPMC10256711 | biostudies-literature

Turbulence activates platelet biogenesis to enable clinical scale manufacturing from human iPS cells

Project description:To identify the genes whose expression levels are changed in VerMES and dish culture, we performed global gene expression analysis of immortalized megakaryocyte cell lines delived from hiPSC.

2018-07-12 | GSE112512 | GEO

Venomics of the desert black cobra Walterinnesia morgani from Çörten village, Turkey

Project description:Combined transcriptomics-assisted bottom-up and top-down MS characterization of the venom proteome of the desert black cobra Walterinnesia morgani from Çörten village, Turkey

2022-02-17 | PXD027497 | Pride

Rett Syndrome in a dish model

Project description:Rett Syndrome in a dish model

| PRJNA419983 | ENA

Canis lupus familiaris strain:Village Dogs

Project description:Canis lupus familiaris strain:Village Dogs Genome sequencing

| PRJNA232497 | ENA