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Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [Hi-C]

ABSTRACT: Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [Hi-C]

PROVIDER: PRJNA562151 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10020434_1.fastq.gz	Fastqsanger.gz
	SRR10020434_2.fastq.gz	Fastqsanger.gz
	SRR10020435_1.fastq.gz	Fastqsanger.gz
	SRR10020435_2.fastq.gz	Fastqsanger.gz
	SRR10020436_1.fastq.gz	Fastqsanger.gz

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Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [Hi-C]

Project description:Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in long-range genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with only a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation but also that there are major structural differences owing to other functions than gene expression. Overall, our results indicate that growth in 3D significantly alters longer-range genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.

2020-09-30 | GSE136306 | GEO

Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions

2020-09-30 | E-MTAB-8303 | biostudies-arrayexpress

Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions

Project description:Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions

| PRJNA562148 | ENA

Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions

Project description:Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions

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Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [RNA-Seq]

Project description:Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [RNA-Seq]

| PRJNA561501 | ENA

Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [RNA-Seq]

2020-09-30 | GSE136173 | GEO

Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions

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

2020-09-30 | GSE136307 | GEO

Compute the Significant Interactions of Hi-C data through HOMER

Project description:Purpose: We can explain the related biological significance from the enhanced proximity in the Hi-C data. Methods: 1. Look for pairs of regions that have more Hi-C reads between them than would be expected by chance. 2.The expected number of reads is calculated using the background model. Result: We found 261,758 significant interactions from H1 cell line and 133,169 significant interactions from IMR90 cell line.

2017-05-09 | GSE93834 | GEO

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Hi-C and Haplotagging datasets for Zemin et al long-range read paper

Project description:Hi-C and Haplotagging datasets for Zemin et al long-range read paper

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