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

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

PROVIDER: PRJNA561501 | ENA |

REPOSITORIES: ENA

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

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 | 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

| PRJEB34277 | 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

| PRJNA562148 | ENA

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

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

| PRJNA562151 | ENA

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

2020-09-30 | GSE136306 | GEO

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

3D Laparoscopy Versus 2D Laparoscopy

Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique. * To evaluate the visual overload in surgeons using 3D laparoscopic technique.

| 2220465 | ecrin-mdr-crc

Clinical randomized study of 3D and 2D laparoscopic radical resection for colorectal cancer.

Project description:Interventions: 2D group:2D laparoscopic surgery;3D group:3D laparoscopic surgery Primary outcome(s): operation time;The amount of bleeding;Number of lymph nodes;Postoperative gastrointestinal function recovery time;Postoperative complications Study Design: Randomized parallel controlled trial

| 2663755 | ecrin-mdr-crc

Expression data from 2D and 3D HepG2 cells

Project description:Expression data from HepG2 cultured in 2D monolayer cultures and 3D Matrigel cultures We performed this study to understand differences in gene expression profiles of 2D and 3D HepG2 cultures

2019-08-31 | GSE128763 | GEO

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