Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin 3D structure in human donor chorion cells

ABSTRACT: chromatin 3D structure in human donor chorion cells

PROVIDER: PRJNA994839 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25276836_1.fastq.gz	Fastqsanger.gz
	SRR25276836_2.fastq.gz	Fastqsanger.gz
	SRR25276837_1.fastq.gz	Fastqsanger.gz
	SRR25276837_2.fastq.gz	Fastqsanger.gz
	SRR25276838_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 34

Similar Datasets

chromatin 3D structure in human donor chorion cells

Project description:Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied high-throughput chromo-some conformation capture technique (Hi-C) to study chromatin 3D structure in human donor chorion cells carrying additional chromosome 13 (Patau syndrome), chromosome 16 (the most common trisomy), and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes 13 and 16, but not 18, results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chro-mosomes, we determined that a limited number of chromosomes change their contact patterns stochastically in trisomic cells, and that it could be linked to LAD and gene content. We also found that genome regions which are more compacted in trisomic cells are significantly enriched in housekeeping genes that potentially suggest the decrease of chromatin accessibility and tran-scription level. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organi-zation.

2023-12-08 | GSE237372 | 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

Dynamic alterations of 3D chromatin structure during differentiation

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

| PRJEB4939 | ENA

Predicting modulaters of TE-driven chromatin 3D structure

Project description:Predicting modulaters of TE-driven chromatin 3D structure

| PRJNA1046126 | ENA

O-GlcNAcylation of CTCF regulates 3D chromatin structure

Project description:O-GlcNAcylation of CTCF regulates 3D chromatin structure

| PRJNA1076940 | 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

Predicting modulaters of TE-driven chromatin 3D structure (HiC)

Project description:Predicting modulaters of TE-driven chromatin 3D structure (HiC)

| PRJNA1046125 | ENA

Predicting modulaters of TE-driven chromatin 3D structure (HiC)

Project description:DNA is tightly packaged in the human nucleus and is wrapped in complex three-dimensional (3D) structures that have been implicated in regulatory processes However, no comprehensive model describes the formation of the 3D genome. At least 40% of the human genome consists of fossilized inactive transposable element (TE) sequences. A role for TEs in 3D genome structure has been suggested by several studies that illustrate how TEs are involved in 3D genome formation. However mechanisms that mediate the formation of TE-mediated 3D contacts is lacking. As TEs are rich in TF binding sites it seems likely that TFs bound to TEs are responsible for forming the 3D genome structure. We used the comprehensive TF binding data available in human and mouse pluripotent stem cells (PSCs), coupled with HiC data to explore the role of TFs bound to TEs in 3D genome organization. Based on these computational predictions we divide TFs into three main classes, those that utilize TEs to drive 3D genome formation, those that are neutral, and a third class that breaks 3D contacts at specific TEs. We then experimentally validate four proteins, and show that SMARCA5 and MAFK are involved in promoting chromatin contacts at TEs, whilst E2F6 and KDM1A are disruptive.

2024-10-26 | GSE248860 | GEO

Donor-to-donor variation in gene expression profile of 3D bronchial epithelial cells after cigarette smoke exposure

Project description:Three-dimensional (3D) cultured primary cells are used to predict the toxicity of substances towards humans because these 3D cultures closely mimic the physiological architecture of tissues. Nonetheless, it is important to consider primary-cell-specific variability for endpoint selection and appropriate evaluation of toxicity because donor-dependent characteristics may be retained even in in vitro cell cultures. In this experiment, 3D differentiated bronchial epithelial cells from three donors were used to investigate donor-to-donor variability, with an aqueous extract of cigarette smoke used as the test substance. Therefore, global gene expression analysis was performed to expand and deepen our insight into the variability.

2022-05-20 | E-MTAB-11316 | 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