Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Consticted migration is associated with stable 3D genome structure differences in cancer cells

ABSTRACT: Consticted migration is associated with stable 3D genome structure differences in cancer cells

PROVIDER: PRJNA601217 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10894100_1.fastq.gz	Fastqsanger.gz
	SRR10894100_2.fastq.gz	Fastqsanger.gz
	SRR10894101_1.fastq.gz	Fastqsanger.gz
	SRR10894101_2.fastq.gz	Fastqsanger.gz
	SRR10894029_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 86

Similar Datasets

Consticted migration is associated with stable 3D genome structure differences in cancer cells (ATAC-Seq)

Project description:Consticted migration is associated with stable 3D genome structure differences in cancer cells (ATAC-Seq)

| PRJNA601213 | ENA

Consticted migration is associated with stable 3D genome structure differences in cancer cells (Hi-C)

Project description:Consticted migration is associated with stable 3D genome structure differences in cancer cells (Hi-C)

| PRJNA601219 | ENA

Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

Project description:Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

| PRJNA601224 | ENA

Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

Project description:We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma cells.

2022-06-29 | GSE143677 | GEO

Consticted migration is associated with stable 3D genome structure differences in cancer cells (ATAC-Seq)

Project description:We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma cells.

2022-06-29 | GSE143674 | GEO

Consticted migration is associated with stable 3D genome structure differences in cancer cells (Hi-C)

Project description:We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma and breast cancer cells.

2022-06-29 | GSE143676 | GEO

Consticted migration is associated with stable 3D genome structure differences in cancer cells

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

2022-06-29 | GSE143678 | GEO

3D chromatin structure in colon cancer

Project description:We report the application of in situ Hi-C technology to 40 colorectal cancer patients and 10 paired-normal tissue to identify CRC specific changes in 3D chromatin structure. The chromatin contact matrices were generated by the sequencing data and image processing/deep learning-based algorithm was proposed to identify long-range abnormal chromatin interaction patterns in the contact matrices. The tumor specific 3D chromatin structure changes and the enhancer-promoter rewiring mediated by the identified chromatin structure changes were analyzed. The complex chromosome-wide rearrangements such as chromothripsis and its effect to 3D chromatin structure were also observed.

2023-07-27 | GSE137188 | GEO

Constricted migration is associated with stable 3D genome structure differences in cancer cells

Project description:To spread from a localized tumor, metastatic cancer cells squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation and DNA repair, here we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.

| S-SCDT-EMBOR-2020-52149-T | biostudies-other

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data