Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamic alterations of 3D chromatin structure during differentiation RNA-seq

ABSTRACT: Dynamic alterations of 3D chromatin structure during differentiation RNA-seq

PROVIDER: PRJEB5012 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR376021.fastq.gz	Fastqsanger.gz
	ERR376022.fastq.gz	Fastqsanger.gz
	ERR376023.fastq.gz	Fastqsanger.gz
	ERR376024.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Dynamic alterations of 3D chromatin structure during differentiation

Project description:Dynamic alterations of 3D chromatin structure during differentiation

| PRJEB4939 | ENA

Dynamic alterations of 3D chromatin structure during differentiation

Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked at long-range via positioning of loci to transcriptionally permissive (euchromatin) or repressive (heterochromatin) environments and at short-range by connecting cis regulatory elements such as promoters and enhancers. However, the dynamics of these processes during cell differentiation still remains unclear. We used Tethered Chromatin Conformation Capture (TCC) to compare the three dimensional chromatin structure of mouse embryonic stem cells (ESC) and neural stem cells (NSC) which we directly derived from the ESC.

2019-08-27 | E-MTAB-2063 | biostudies-arrayexpress

Dynamic alterations of 3D chromatin structure during differentiation RNA-seq

2019-08-27 | E-MTAB-2125 | biostudies-arrayexpress

Dynamic chromatin structure during early ILC progenitor differentiation

Project description:Dynamic chromatin structure during early ILC progenitor differentiation

| PRJNA527826 | ENA

KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure

Project description:Neural differentiation of embryonic stem cells (ESCs) requires precisely orchestrated gene regulation, a process governed in part by changes in 3D chromatin structure. How these changes regulate gene expression in this context remains unclear. In this study, we observed enrichment of the transcription factor KLF4 at some poised or closed enhancers at TSS-linked regions of genes associated with neural differentiation, such as Pax6. Combination analysis employing ChIP, HiChIP and RNA-seq data indicated that KLF4 loss in ESCs induced changes in 3D chromatin structure, including increased chromatin interaction loops between neural differentiation-associated genes and active enhancers. And changes of chromatin structure upregulated expression of neural differentiation-associated genes and promoted early neural differentiation. This study reveals that KLF4 has a differentiation inhibitory effect in regulating 3D chromatin structure and suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation.

2022-06-01 | GSE194068 | GEO

KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure, a new mechanism of early neural differentiation

Project description:Circular RNA has been reported to be dynamically expressed during embryonic development and regulates human embryonic stem cells (hESCs), but the identification and regulation of functional circular RNA in mouse embryonic stem cells (mESC) remains unclear. Neural differentiation of embryonic stem cells (ESCs) requires precisely orchestrated gene regulation, a process governed in part by changes in 3D chromatin structure. How these changes regulate gene expression in this context remains unclear. In this study, we observed enrichment of the transcription factor KLF4 at some poised or closed enhancers at TSS-linked regions of genes associated with neural differentiation. Combination analysis of ChIP, HiChIP and RNA-seq data indicated that KLF4 loss in ESCs induced changes in 3D chromatin structure, including increased chromatin interaction loops between neural differentiation-associated genes and active enhancers, leading to upregulated expression of neural differentiation-associated genes and therefore early neural differentiation. This study suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation. Conclusions: Our study suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation.

2022-09-20 | GSE213418 | GEO

Two enhancers synergistically regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure

Project description:Homeobox B cluster (HoxB) genes play important roles in RA-induced early ESCs differentiation. In this study, we identified two enhancers synergistically regulate HoxB genes expressions through 3D chromatin structure and thus regulate RA-induced early ESCs differentiation. 4C data showed interactions between HoxB genes and the two enhancers. CRISPR/Cas9-mediated individual or compound deletion of the two enhancers significantly inhibits HoxB genes expressions while transcriptome analysis revealed that RA induced early ESCs differentiation was blocked in the enhancer KO cells. Our study suggests new mechanism by which two enhancers regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure.

2021-03-01 | GSE165725 | 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

3D chromatin structure in colon cancer

Project description:3D chromatin structure in colon cancer

| PRJNA564773 | ENA

KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure

Project description:KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure

| PRJNA798967 | ENA